This doubt is based on the narration wherein there is mention that when the killing of Muhammad ibn Abi Bakr reached Aisha radiya Llahu ‘anha, she read qunut and prayed against Muawiyah and ‘Amr ibn al ‘As radiya Llahu ‘anhuma after every salah.
This doubt can be answered in two ways:
This incident has been recorded by al Tabari as follows:
قال أبو مخنف فحدثني محمد بن يوسف بن ثابت الأنصاري عن شيخ من أهل المدينة قال كتب محمد بن أبي بكر إلى معاوية بن أبي سفيان جواب كتابه أما بعد فقد أتاني كتابك تذكرني من أمر عثمان أمرا لا أعتذر إليك منه وتأمرني بالتنحي عنك كأنك لي ناصح وتخوفني المثلة كأنك شفيق وأنا أرجو أن تكون لي الدائرة عليكم فأجتاحكم في الوقعة …وخرج محمد في ألفي رجل واستقبل عمرو بن العاص كنانة وهو على مقدمة محمد فأقبل عمرو نحو كنانة فلما دنا من كنانة سرح الكتائب كتيبة بعد كتيبة فجعل كنانة لا تأتيه كتيبة من كتائب أهل الشام إلا شد عليها بمن معه فيضربها حتى يقربها لعمرو بن العاص ففعل ذلك مرارا فلما رأى ذلك عمرو بعث إلى معاوية بن حديج السكوني فأتاه في مثل الدهم فأحاط بكنانة وأصحابه واجتمع أهل الشام عليهم من كل جانب فلما رأى ذلك كنانة بن بشر نزل عن فرسه ونزل أصحابه وكنانة يقول وما كان لنفس أن تموت إلا بإذن الله كتابا مؤجلا ومن يرد ثواب الدنيا نؤته منها ومن يرد ثواب الآخرة نؤته منها وسنجزي الشاكرين فصار بهم بسيفه حتى استشهد رحمه الله وأقبل عمرو بن العاص نحو محمد بن أبي بكر وقد تفرق عنه أصحابه لما بلغهم قتل كنانة حتى بقي وما معه أحد من أصحابه فلما رأى ذلك محمد خرج يمشي في الطريق حتى انتهى إلى خربة في ناحية الطريق فأوى إليها وجاء عمرو بن العاص حتى دخل الفسطاط وخرج معاوية بن حديج في طلب محمد حتى انتهى إلى علوج في قارعة الطريق فسألهم هل مر بكم أحد تنكرونه فقال أحدهم لا والله إلا أني دخلت تلك الخربة فإذا أنا برجل فيها جالس فقال ابن حديج هو هو ورب الكعبة فانطلقوا يركضون حتى دخلوا عليه فاستخرجوه وقد كاد يموت عطشا فأقبلوا به نحو فسطاط مصر قال ووثب أخوه عبد الرحمن بن أبي بكر إلى عمرو بن العاص وكان في جنده فقال أتقتل أخي صبرا ابعث إلى معاوية بن حديج فانهه فبعث إليه عمرو بن العاص يأمره أن يأتيه بمحمد بن أبي بكر فقال معاوية أكذاك! قتلتم كنانة بن بشر وأخلي أنا عن محمد بن أبي بكر هيهات أكفاركم خير من أولئكم أم لكم براءة في الزبر
فقال لهم محمد اسقوني من الماء قال له معاوية بن حديج لا سقاه الله إن سقاك قطرة أبدا إنكم منعتم عثمان أن يشرب الماء حتى قتلتموه صائما محرما فتلقاه الله بالرحيق المختوم والله لأقتلنك يا ابن أبي بكر… فغضب معاوية فقدمه فقتله ثم ألقاه في جيفة حمار ثم أحرقه بالنار فلما بلغ ذلك عائشة جزعت عليه جزعا شديدا وقنتت عليه في دبر الصلاة تدعو على معاوية وعمرو
وذكر الواقدي انه لما قتل كنانه بن بشر بن عتاب التجيبي فهرب عند ذالك محمد بن أبي بكر فاختبأ عند جبلة بن مسروق فدل عليه فجاء معاوية بن حديج وأصحابه فأحاط به فخرج اليهم محمد ن أبي بكر فقاتل حتى قتل.
According to Abu Mikhnaf — from Muhammad ibn Yusuf ibn Thabit al Ansari — from a sheikh of the people of al Madinah:
Muhammad ibn Abi Bakr wrote to Muawiyah ibn Abi Sufyan in reply to his letter:
I have received your letter in which you remind me of the matter of ‘Uthman, and I make no apology to you regarding that. You tell me to withdraw from you, as if you were a sincere adviser, and you try to frighten me with reference to an exemplary punishment (al muthlah) as if you were sympathetic to me. I hope that fortune will raise me up again over you and that I will sweep you away in battle…
Muhammad went out with two thousand men whilst ‘Amr ibn al ‘As went to meet Kinanah, who was over the vanguard of Muhammad, and he proceeded toward him. When he drew near to Kinanah, he dispatched the squadrons, one after another. Whenever one of the Syrian squadrons approached him, Kinanah would attack it with the men he had with him and assail it so as to force it to draw near again to ‘Amr ibn al ‘As. He did that several times and ‘Amr, seeing it, sent for Muawiyah ibn Hudayj al Sakuni, who came with a sizable force and surrounded Kinanah and his men. Then the Syrians gathered against them on all sides and, when Kinanah ibn Bishr perceived that, he dismounted together with his men, saying:
And it is not [possible] for one to die except by permission of Allah at a decree determined. And whoever desires the reward of this world – We will give him thereof; and whoever desires the reward of the Hereafter – We will give him thereof. And We will reward the grateful.
And he fought the Syrians with his sword until he fell a martyr, may Allah have mercy upon him.
‘Amr ibn al ‘As advanced toward Muhammad ibn Abi Bakr, whose men had deserted. When Muhammad perceived that, he went off on foot along the road until he came to a ruined place close to it and sought shelter there.
‘Amr ibn al ‘As proceeded to occupy al Fustat while Muawiyah ibn Hudayj went off in pursuit of Muhammad. He came upon some local non-Arabs on the highway and asked them, “Did anyone unknown to you pass by?”
One of them replied, “No, by God, but I went in to this ruined place and I saw a man sitting in it.”
Ibn Hudayj said, “By the Lord of the Ka’bah, that is he;”
He rushed forward and went to him. They brought him out almost dead of thirst and took him off toward Fustat of Egypt.
Muhammad’s brother, ‘Abdur Rahman ibn Abi Bakr, who was part of the army of ‘Amr ibn al ‘As, hurried to ‘Amr and said, “Will you kill my brother in chains? Send to Muawiyah ibn Hudayj and forbid him to do that.”
So ‘Amr sent to him, telling him to bring Muhammad ibn Abi Bakr to him, but Muawiyah said, “Really! You have killed Kinanah ibn Bishr and I should let Muhammad ibn Abi Bakr go! What an idea!
Are your disbelievers better than those, or have you immunity in the scriptures?
Muhammad said to them, “Give me some water to drink.” but Muawiyah ibn Hudayj answered him, “May Allah not give him anything to drink if he ever gives you a drop. You prevented ‘Uthman from drinking water until you had killed him, while he was fasting and in a state of ritual purity, and Allah received him with ‘choice sealed wine’ By Allah! I will kill you, Ibn Abi Bakr.”
Muawiyah became angry, had him brought forward, and killed him. Then he cast him into the corpse of a donkey and set fire to it. When Aisha heard about that, she mourned for him greatly and made qunut for him at the end of the prayers, appealing to Allah against Muawiyah and ‘Amr.
According to al Waqidi:
When Kinanah ibn Bishr ibn ‘Attab al Tujibi was killed and he could find no more men, Muhammad ibn Abi Bakr fled and tried to hide with Jabalah ibn Masruq. But Muawiyah ibn Hudayj was led to him and surrounded him, and Muhammad then came out and fought until he was killed.
This incident is extremely weak.
Abu Mikhnaf, Lut ibn Yahya
Muhammad ibn Yusuf ibn Thabit ibn Qais ibn Shammas
He is mentioned in the books of biographical collections as Yusuf ibn Muhammad.
Sheikh of the people of al Madinah
This is the person narrating from Muhammad ibn Abi Bakr in the chain. ‘A Sheikh’ is ambiguous. And ambiguity is a type of weak narration, since the narrator is not known at all, forget his status as a narrator.
Thus, the narration is extremely weak and is not fit to be presented as evidence.
If, for arguments sake, we accept the narration then the following issues need to be considered:
Muawiyah ibn Hudayj killed him in retaliation for killing ‘Uthman. Yes, Muhammad ibn Abi Bakr did enter the house of ‘Uthman but he did not kill him.
Ibn Kathir said:
الصحيح أن الذي فعل ذلك غيره وأنه استحیی ورجع حين قال له عثمان لقد أخذت بلحية كان أبوك يكرمها فتذمم من ذلك وغطى وجهه ورجع وحاجز دونه فلم يفد وكان أمر الله قدراً مقدوراً وكان ذلك في الكتاب مسطوراً
The truth of the matter is that others committed the heinous crime and he was not involved. He felt ashamed and went back when ‘Uthman addressed him saying, “You have grabbed a beard which your father used to honour.” He felt ashamed and went back, and he regretted his actions and covered his face, and he tried to defend him, but to no avail.
— If we consider Aisha radiya Llahu ‘anha praying against Muawiyah and ‘Amr ibn al ‘As radiya Llahu ‘anhuma for the killing of her brother to be a factual, then that would have been a natural, human reaction. Any person would feel pain on hearing the news of their brother or dear one being killed and resort to praying against them. That being said, the one to kill Muhammad ibn Abi Bakr was Muawiyah ibn Hudayj. This is supported by the following narration of Sahih Muslim on the authority of ‘Abdur Rahman ibn Shamasah. She asked him when he came to her:
ممن أنت فقلت رجل من أهل مصر فقالت كيف كان صاحبكم لكم في غزاتكم هذه فقال ما نقمنا منه شيئا إن كان ليموت للرجل منا البعير فيعطيه البعير والعبد فيعطيه العبد ويحتاج إلى النفقة فيعطيه النفقة فقالت أما إنه لا يمنعني الذي فعل في محمد بن أبي بكر أخي أن أخبرك ما سمعت من رسول الله صلى الله عليه وسلم يقول في بيتي هذا اللهم، من ولي من أمر أمتي شيئا فشق عليهم فاشقق عليه ومن ولي من أمر أمتي شيئا فرفق بهم فارفق به
“Where are you from?”
He replied, “From the people of Egypt.”
She said, “How did your leader treat you in this war?”
He replied, “We did not disapprove any action of his. If any of our men’s camel died, he would give him a camel. If a slave died, he would give him a slave. If anyone needed money, he would give him the same.”
She said, “Harken! His treatment of Muhammad ibn Abi Bakr, my brother, will not prevent me from informing you of what I heard from the Messenger of Allah salla Llahu ‘alayhi wa sallam which he pronounced in this house of mine, ‘O Allah, whoever gains authority of any portion of my Ummah and is harsh towards them, then display harshness towards him. And if anyone gains authority of any portion of my Ummah and treats them compassionately, then treat him with compassion.’”
His name is mentioned unequivocally in Musnad Abi ‘Uwanah.
The narration of al Bayhaqi is as follows, “How did ibn Hudayj treat you in this war?”
— If this narration is taken at face value, it shows ‘Amr ibn al ‘As making attempts to save the life of Muhammad and, thus, he cannot be censured.
— Muawiyah radiya Llahu ‘anhu had exercised his ijtihad in fighting ‘Ali radiya Llahu ‘anhu. He saw himself to be in the right, seeking to avenge the blood of ‘Uthman radiya Llahu ‘anhu as his relative. And since Muhammad ibn Abi Bakr was amongst those who entered the house of ‘Uthman radiya Llahu ‘anhu, he would have been liable, according to Muawiyah and his camp, for the murder of ‘Uthman radiya Llahu ‘anhu as well.
— According to Aisha radiya Llahu ‘anha, Muhammad was killed unjustly by the camp of Muawiyah radiya Llahu ‘anhu. If she prayed against him, then she is a Sahabiyyah and he is a Sahabi. What benefit would we derive from discussing the matter and involving ourselves in it?
— The reality of the matter will be unveiled in the Day of Qiyamah. Allah subhanahu wa ta ‘ala says:
ثُمَّ إِنَّكُمْ يَوْمَ ٱلْقِيَـٰمَةِ عِنْدَ رَبِّكُمْ تَخْتَصِمُوْنَ
Then indeed you, on the Day of Resurrection, before your Lord, will dispute.
This wasn’t the first difference of opinion between the Sahabah radiya Llahu ‘anhum. They were human and not infallible. That being said, it is not up to us to judge them. All of their matters will be presented before Allah subhanahu wa ta ‘ala:
إِنَّ إِلَيْنَآ إِيَابَهُمْ ثُمَّ إِنَّ عَلَيْنَا حِسَابَهُم
Indeed, to Us is their return. Then indeed, upon Us is their account.
Our responsibility is to revere and respect them. Sure, they may have erred but we do not delve into it, nor do we seek to censure them for it due to the status they enjoy in the sight of Allah subhanahu wa ta ‘ala. Allah subhanahu wa ta ‘ala chose them to be the Companions of his Messenger salla Llahu ‘alayhi wa sallam. He has praised them thus:
مُّحَمَّدٌ رَّسُولُ اللّٰهِ وَالَّذِيْنَ مَعَهُ أَشِدَّاءُ عَلَى الْكُفَّارِ رُحَمَاءُ بَيْنَهُمْ تَرَاهُمْ رُكَّعًا سُجَّدًا يَّبْتَغُونَ فَضْلًا مِّنَ اللّٰهِ وَرِضْوَانًا سِيْمَاهُمْ فِيْ وُجُوْهِهِم مِّنْ أَثَرِ السُّجُودِ ذٰلِكَ مَثَلُهُمْ فِي التَّوْرَاةِ وَمَثَلُهُمْ فِي الْإِنْجِيْلِ كَزَرْعٍ أَخْرَجَ شَطْأَهُ فَأٰزَرَهُ فَاسْتَغْلَظَ فَاسْتَوَىٰ عَلٰى سُوْقِهِ يُعْجِبُ الزُّرَّاعَ لِيَغِيْظَ بِهِمُ الْكُفَّارَ وَعَدَ اللّٰهُ الَّذِيْنَ أٰمَنُوا وَعَمِلُوا الصَّالِحَاتِ مِنْهُم مَّغْفِرَةً وَّأَجْرًا عَظِيْمًا
Muhammad is the Messenger of Allah; and those with him are forceful against the disbelievers, merciful among themselves. You see them bowing and prostrating [in prayer], seeking bounty from Allah and [His] pleasure. Their sign is in their faces from the effect of prostration [i.e., prayer]. That is their description in the Torah. And their description in the Gospel is as a plant which produces its offshoots and strengthens them so they grow firm and stand upon their stalks, delighting the sowers, so that He [i.e., Allah] may enrage by them1 the disbelievers. Allah has promised those who believe and do righteous deeds among them forgiveness and a great reward.
Rasulullah salla Llahu ‘alayhi wa sallam also praised them. He anointed their era the best of all eras and prohibited from censuring and reviling them.
 Ibn Abi al Hadid: Sharh Nahj al Balaghah, vol. 6 pg. 72; al Amini: al Ghadir, vol. 2 pg. 133.
 Al Tabari: Tarikh al Rusul, vol. 3 pg. 131.
 Surah Al ‘Imran: 145.
 Ibn al Kathir in Al Bidayah wa al Nihayah, vol. 10 pg. 661.
 Abu Dawood: al Sunan: 3887.
 Al Jarh wa al Ta’dil, vol. 9 pg. 222.
 Al Mizan, vol. 4 pg. 472.
 Al Taqrib: 7879.
 Ibn Kathir: Al Bidayah wa al Nihayah, vol. 10 pg. 308. This narration has been recorded with a complete chain (Musnad) by ibn Abi Shaybah in al Musannaf, vol. 15 pg. 219; Khalifah: Al Tarikh, vol. 1 pg. 39; Ibn Hambal: Al Fada’il, vol. 1 pg. 472; Ibn Shabbah: Tarikh al Madinah al Munawwarah, vol. 4 pg. 1285; and Al Tabari: Tarikh al Rusul, vol. 1pg. 384.
 Sahih Muslim, Kitab al Imarah, chapter regarding the virtue of a just leader and the punishment of an oppressive ruler: 1828.
 Musnad Abi ‘Uwanah, vol. 4 pg. 381.
 Al Sunan, vol. 9 pg. 43.
 Surah al Zumar: 31.
 Surah al Ghashiyah: 26.
 Surah al Fath: 29.
 See the foreword of the book for further reading.