وَاقْتُلُوهُمْ حَيْثُ ثَقِفْتُمُوهُمْ وَأَخْرِجُوهُم مِّنْ حَيْثُ أَخْرَجُوكُمْ ۚ وَالْفِتْنَةُ أَشَدُّ مِنَ الْقَتْلِ ۚ وَلَا تُقَاتِلُوهُمْ عِندَ الْمَسْجِدِ الْحَرَامِ حَتَّىٰ يُقَاتِلُوكُمْ فِيهِ ۖ فَإِن قَاتَلُوكُمْ فَاقْتُلُوهُمْ ۗ كَذَٰلِكَ جَزَاءُ الْكَافِرِينَ (191)
(2:191) Fight against them wherever they confront you in combat and drive them out from where they drove you out. Though killing is bad. persecution is worse than killing *202 Do not fight against them near the Masjid Haram unless they attack you there.
*202). Here the word fitnah is used in the sense of 'persecution'. It refers to a situation whereby either a person or a group is subjected to harassment and intimidation for having accepted, as true, a set of ideas contrary to those currently held, and for striving to effect reforms in the existing order of society by preaching what is good and condemning what is wrong. Such a situation must be changed, if need be, by the force of arms.
Bloodshed is bad, but when one group of people imposes its ideology and forcibly prevents others from accepting the truth, then it becomes guilty of an even more serious crime. In such circumstances, it is perfectly legitimate to remove that oppressive group by the force of arms.