I think setting Heartless on people and stealing hearts would constitute being evil.
Most Nukige are rape focused? That's a completely false claim, as proven below.
If you include rape and nukige, the results are thus:
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Thirty pages. Now that's a lot. But if you exclude rape and keep nukige:
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Sixty four pages. So consensual nukige more than doubles the ones with rape, and the ones with rape don't necessarily even have rapist protagonists.
He doesn't gotta be evil. Nobody ever said he had to. Honestly, ever since Four Elements Trainer, I'm down for either. Good writing is, in and of itself, a good enough reason to play a game for me. But I still lean towards immoral protagonists, as do most of F95, I think.