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;
وَلَا 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 وَالاَْرْضَ 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 إِلاَّ 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.
لاا يُعْضَدُ شَجَرُهُ وَلَا يُخْتَلىَ خَلَهُ
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 امِنٌ وَمَنْ دَخَلَ الْمَسْجِدَ فَهُو امِنٌ ومَنْ دَخَلَ دَارَ أَبِي سُفْيَانَ فَهُوَ امِن
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
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,
وَلَوْلَا رِجَالٌ مُّوْمِنُونَ وَنِسَأءٌ مُّوْمِنَـتٌ لَّمْ تَعْلَمُوهُمْ أَن تَطَيُوهُمْ فَتُصِيبَكمْ مِّنْهُمْ مَّعَرَّةٌ بِغَيْرِ عِلْمٍ لِّيُدْخِلَ اللَّهُ فِى رَحْمَتِهِ مَن يَشَأءُ 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)
Allah's statement;
فَإِنِ انتَهَوْاْ فَإِنَّ اللّهَ غَفُورٌ رَّحِيمٌ