The persecution of witches targeted individuals or small groups, not (as far as modern history knows) members of any particular religion; and the charges leveled at alleged witches usually involved sorcerous misbehavior of various kinds (blighting crops, causing storms, bringing pestilence...) rather than purely religious accusations. Indeed, for most of the medieval era the Church denied the existence of witches (though, as we've seen above, it was happy to persecute real heretics): witch trials only gained substantial clerical backing well into the early modern period.
Seems pretty different to me.
Charges of being in league with the Devil were a necessary part of accusations against the witches because, I think, sorcery was considered to be possible for humans only through the Devil's help. The witches' covens were perceived as actively worshipping the Devil.
I agree that it's not the exact parallel, but do you think a whole community (with towns and everything) of devil worshippers could have survived in Europe or North America for any significant period of time? Compared to Islam, Christianity was just more quick and efficient about eliminating them.
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