Abu Jafar Ar-Razi said that Ar-Rabi bin Anas said that Abu Al-Aliyah commented on what Allah said: وَقَاتِلُواْ فِي سَبِيلِ اللّهِ الَّذِينَ يُقَاتِلُونَكُمْ (And fight in the way of Allah those who fight you),
"This was the first Ayah about fighting that was revealed in Al-Madinah. Ever since it was revealed, Allah's Messenger used to fight only those who fought him and avoid non-combatants. Later, Surah Bara'h was revealed.''
Abdur-Rahman bin Zayd bin Aslam said similarly, then he said that; this was later abrogated by the Ayah: فَاقْتُلُواْ الْمُشْرِكِينَ حَيْثُ وَجَدتُّمُوهُمْ (then kill them wherever you find them), (9:5).
However, this statement is not plausible, because Allah's statement: الَّذِينَ يُقَاتِلُونَكُمْ (...those who fight you) applies only to fighting the enemies who are engaged in fighting Islam and its people. So the Ayah means,
`Fight those who fight you', just as Allah said in another Ayah: وَقَاتِلُواْ الْمُشْرِكِينَ كَآفَّةً كَمَا يُقَاتِلُونَكُمْ كَآفَّةً (...and fight against the Mushrikin collectively as they fight against you collectively), (9:36).
This is why Allah said later in the Ayah: وَاقْتُلُوهُمْ حَيْثُ ثَقِفْتُمُوهُمْ وَأَخْرِجُوهُم مِّنْ حَيْثُ أَخْرَجُوكُمْ (And kill them wherever you find them, and turn them out from where they have turned you out), meaning, `Your energy should be spent on fighting them, just as their energy is spent on fighting you, and on expelling them from the areas from which they have expelled you, as a law of equality in punishment.'
The Prohibition of mutilating the Dead and stealing from the captured Goods
Allah said:
... وَلاَ تَعْتَدُواْ إِنَّ اللّهَ لاَ يُحِبِّ الْمُعْتَدِينَ
but transgress not the limits. Truly, Allah likes not the transgressors.
This Ayah means,
`Fight for the sake of Allah and do not be transgressors,' such as, by committing prohibitions.
Al-Hasan Al-Basri stated that transgression (indicated by the Ayah), "includes mutilating the dead, theft (from the captured goods), killing women, children and old people who do not participate in warfare, killing priests and residents of houses of worship, burning down trees and killing animals without real benefit.''
This is also the opinion of Ibn Abbas, Umar bin Abdul-Aziz, Muqatil bin Hayyan and others.
Muslim recorded in his Sahih that Buraydah narrated that Allah's Messenger said:
اغْزُوا فِي سَبِيلِ اللهِ، قَاتِلُوا مَنْ كَفَرَ بِاللهِ، اغْزُوا وَلَا تَغُلُّوا وَلَا تَغْدِرُوا وَلَا تَمْثُلُوا وَلَا تَقْتُلُوا وَلِيدًا وَلَا أَصْحَابَ الصَّوَامِع
Fight for the sake of Allah and fight those who disbelieve in Allah. Fight, but do not steal (from the captured goods), commit treachery, mutilate (the dead), or kill a child, or those who reside in houses of worship.
It is reported in the Two Sahihs that Ibn Umar said,
"A woman was found dead during one of the Prophet's battles and the Prophet then forbade killing women and children.''
There are many other Hadiths on this subject.
Shirk is worse than Killing
Allah says;
وَاقْتُلُوهُمْ حَيْثُ ثَقِفْتُمُوهُمْ وَأَخْرِجُوهُم مِّنْ حَيْثُ أَخْرَجُوكُمْ وَالْفِتْنَةُ أَشَدُّ مِنَ الْقَتْلِ ...
And kill them wherever you find them, and turn them out from where they have turned you out. And Al-Fitnah is worse than killing.
Since Jihad involves killing and shedding the blood of men, Allah indicated that these men are committing disbelief in Allah, associating with Him (in the worship) and hindering from His path, and this is a much greater evil and more disastrous than killing.
Abu Malik commented about what Allah said: وَالْفِتْنَةُ أَشَدُّ مِنَ الْقَتْلِ (And Al-Fitnah is worse than killing), "meaning what you (disbelievers) are committing is much worse than killing.''
Abu Al-Aliyah, Mujahid, Sa`id bin Jubayr, Ikrimah, Al-Hasan, Qatadah, Ad-Dahhak and Ar-Rabi bin Anas said that what Allah said: وَالْفِتْنَةُ أَشَدُّ مِنَ الْقَتْلِ (And Al-Fitnah is worse than killing),
"Shirk (polytheism) is worse than killing.''
Fighting in the Sacred Area is prohibited, except in Self-Defense
Allah said:
... وَلاَ تُقَاتِلُوهُمْ عِندَ الْمَسْجِدِ الْحَرَامِ ...
And fight not with them at Al-Masjid Al-Haram (the sanctuary at Makkah).
It is reported in the Two Sahihs that the Prophet said:
إنَّ هَذَا الْبَلَدَ حَرَّمَهُ اللهُ يَوْمَ خَلَقَ السَّموَاتِ وَالْأَرْضَ، فَهُوَ حَرَامٌ بِحُرْمَةِ اللهِ إِلى يَوْمِ الْقِيَامَةِ،
Allah has made this city a sanctuary since the day He created the heavens and the earth. So, it is a sanctuary by Allah's decree till the Day of Resurrection.
وَلَمْ يَحِلَّ لِي إِلَّا سَاعَةً مِنْ نَهَارٍ، وَإِنَّهَا سَاعَتِي هذِهِ حَرامٌ بحُرْمَةِ اللهِ إِلى يَوْمِ الْقِيامَةِ،
Fighting in it was made legal for me only for an hour in the daytime. So, it (i.e., Makkah) is a sanctuary, by Allah's decree, from now on until the Day of Resurrection.
لا يُعْضَدُ شَجَرُهُ، وَلَا يُخْتَلىَ خَلَاهُ،
Its trees should not be cut, and its grass should not be uprooted.
فَإِنْ أَحَدٌ تَرَخَّصَ بِقِتَالِ رَسُولِ اللهِصلى الله عليه وسلّم، فَقُولُوا: إنَّ اللهَ أَذِنَ لِرَسُولِهِ وَلَمْ يَأْذَنْ لَكُم
If anyone mentions the fighting in it that occurred by Allah's Messenger, then say that Allah allowed His Messenger, but did not allow you. In this Hadith, Allah's Messenger mentions fighting the people of Makkah when he conquered it by force, leading to some deaths among the polytheists in the area of the Khandamah. This occurred after the Prophet proclaimed:
مَنْ أَغْلَقَ بَابَهُ فهُوَ آمِنٌ،وَمَنْ دَخَلَ الْمَسْجِدَ فَهُو آمِنٌ، ومَنْ دَخَلَ دَارَ أَبِي سُفْيَانَ فَهُوَ آمِن
Whoever closed his door is safe. Whoever entered the (Sacred) Mosque is safe. Whoever entered the house of Abu Sufyan is also safe.
Allah said:
... حَتَّى يُقَاتِلُوكُمْ فِيهِ فَإِن قَاتَلُوكُمْ فَاقْتُلُوهُمْ كَذَلِكَ جَزَاء الْكَافِرِينَ ﴿١٩١﴾
...unless they (first) fight you there. But if they attack you, then kill them. Such is the recompense of the disbelievers.
Allah states:
`Do not fight them in the area of the Sacred Mosque unless they start fighting you in it. In this case, you are allowed to fight them and kill them to stop their aggression.'
Hence, Allah's Messenger took the pledge from his Companions under the tree (in the area of Al-Hudaybiyyah) to fight (the polytheists), after the tribes of Quraysh and their allies, Thaqif and other groups, collaborated against the Muslims (to stop them from entering Makkah to visit the Sacred House). Then, Allah stopped the fighting before it started between them and said:
وَهُوَ الَّذِى كَفَّ أَيْدِيَهُمْ عَنكُمْ وَأَيْدِيَكُمْ عَنْهُم بِبَطْنِ مَكَّةَ مِن بَعْدِ أَنْ أَظْفَرَكُمْ عَلَيْهِمْ
And He it is Who has withheld their hands from you and your hands from them in the midst of Makkah, after He had made you victors over them. (48:24)
and,
وَلَوْلاَ رِجَالٌ مُّؤْمِنُونَ وَنِسَآءٌ مُّؤْمِنَـتٌ لَّمْ تَعْلَمُوهُمْ أَن تَطَئُوهُمْ فَتُصِيبَكمْ مِّنْهُمْ مَّعَرَّةٌ بِغَيْرِ عِلْمٍ لِّيُدْخِلَ اللَّهُ فِى رَحْمَتِهِ مَن يَشَآءُ لَوْ تَزَيَّلُواْ لَعَذَّبْنَا الَّذِينَ كَفَرُواْ مِنْهُمْ عَذَاباً أَلِيماً
Had there not been believing men and believing women whom you did not know, that you may kill them and on whose account a sin would have been committed by you without (your) knowledge, that Allah might bring into His mercy whom He wills ـ if they (the believers and the disbelievers) had been apart, We verily, would have punished those of them who disbelieved with painful torment. (48:25)