No one is out there forcefully deconverting Muslims because of their belief in atheism.
Assuming you’re talking about China, they are doing to for control. They don’t want a part of their population following someone or something else except the state.
And the Crusades were done out of a lust for more land, and sexual assault of minors were done because some priests are also pedophiles. You can’t No True Scotsman this way because all of these ideologies can be used as excuses for justifying heinous actions.
It doesn’t make it magically not a part of the problem, and I think that’s what people have been saying about the terrible practices in religion as long as there’s been this problem. It would be hypocritical and disingenuous to downplay the way that atheism and secularity has been used to justify extreme behaviour - the idea that atheism gives rise to only the nicest extremists is such a silly hill to die on.