But she didn't kill him to stop him becoming a Christian leader, she killed him so that he wouldn't steal her childhood and make her into a mass murderer. The ending how it shipped borrows Christian themes with him being "baptised" in the river wiping away his sins in a literal sense in that his sins literally never happened. Nothing in the game says Christianity is bad just that nut jobs that use religion to manipulate and control people to further their own desires are just that, there are plenty of real world examples of that stuff happening using many different religions. Your homosexuality scenario really doesn't work the same way at all, and you can't stop yourself becoming homosexual anyway.
Maybe the original ending was offensive, but the current one is pretty damn tame. If anything your post is probably more offensive to homosexual people than the game is to Christians.
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