Waqatiloohum hatta la takoona fitnatun wayakoona addeenu lillahi fa-ini intahaw fala AAudwana (surah Baqarah: 193)

Tafseer Tafheem-ul-Quran by Syed Abu-al-A'la Maududi

(2:193) Go on fighting with them till there is no more a state of tribulation and Allah's way is established instead. *204 Then if they desist from it, there should be no more hostility except against those who had been guilty of cruelty and brutality. *205

Wa qaatiloohum hatta laa takoona fitnatunw wa yakoonad deenu lillaahi fa-inin tahaw falaa `udwaana illaa `alaz zaalimeen

*204). Here the term fitnah is used in a different sense from the one in which it was used above (see verse 191). It is evident from the context that fitnah refers here to the state of affairs wherein the object of obedience is someone other than God. Hence the purpose of a believer's fighting is that this fitnah should cease and obedience should be consecrated to God alone.
An investigation of the usages of the word din (which occurs in this verse) reveals that the core of its meaning is obedience. In its technical usage, the word refers to that systern of life which arises as a result of a person recognizing someone as his Lord and Sovereign and committing himself to following his commands and ordinances. This explanation of the word din makes it quite clear that when some human beings establish their godhead and absolute dominance over others, this state of affairs is one of fitnah. Islam seeks to put an end to this and replace it by a state of affairs in which people live in obedience to the laws of God alone.
*205). What is meant here by 'desisting' is not the abandonment of unbelief and polytheism on the part of the unbelievers but rather their desistance from active hostility to the religion enjoined by God. The unbeliever, the polytheist, the atheist, has each been, empowered to hold on to his beliefs and to woorship who and whatever he wishes. In order to deliver these people from their error, Muslims are required to counsel them and tell them where their good lies. But Muslims ought not to try to achieve this purpose by resorting to force. At the same time, these misguided people have no right to either enforce the false laws of their own contriving instead of the laws of God or to drive the people of God to bondage of others than God. In order to put an end to this fitnah, both persuasion and force be used, whenever and to the extent to which each of the two is needed, and a true believer will not rest until the unbelievers give up this fitnah.
The statement that hostility is meant only against wrong-doers seems to imply that when the true system of life replaces the false one, ordinary people should be granted a general amnesty. At the same time, however, it would be justifiable to punish those who exceeded all limits in their hostility to the Truth, at the time when they held the reins of power. Yet in dealing with such people, it becomes the true believers, after they have one final victory, to adopt a general attitude of forgiveness and tolerance towards the vanquished rather than subject them to revenge for the wrongs they committed in the past. Those criminals whose records were exceptionally bad could, however, be punished. The Prophet (peace be on him), availed himself of this permission in respect of some notorious enemies whose hostility had exceeded all limits, even though pardon and forgiveness behoved none more than him. Thus 'Uqbah ibn Abi Mu'avt and Nadr b. Harith from among the captives of the Battle of Badr were put to death and when a general amnesty, was proclaimed after the conquest of Makka four out of seventeen persons were executed. (See Ibn Hisham, vol. 1, p. 644 and vol. 2, pp. 409 ff. - Ed.) These acts were based on the permission to put to the sword those who have been conspicuously ruthless in their hostility to Islam and the Muslims.