It is evident reading the verse in its contextual setting that the passage does not encourage indiscriminate violence against disbelievers, just because of their faith. Verse 4:90 tells Muslims that if the disbelievers moved away and ceased hostilities against the Muslims, that they, the disbelievers be left alone.
They wish you would disbelieve as they disbelieved so you would be alike. So do not take from among them allies until they emigrate for the cause of Allah. But if they turn away, then seize them and kill them wherever you find them and take not from among them any ally or helper. – Quran 4:89
The above verse is used and manipulated by critics to show that Muslims are allowed to wage war against disbelievers. However, reading the verse that proceeds after, verse 4:90, states the following,
4:90 Except for those who take refuge with a people between yourselves and whom is a treaty or those who come to you, their hearts strained at [the prospect of] fighting you or fighting their own people. And if Allah had willed, He could have given them power over you, and they would have fought you. So if they remove themselves…
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