Hmm...bizarrely enough, Fire Emblem: Radiant Dawn probably qualifies even though (major spoilers starting here and going throughout the remainder of this post) the final boss is the world's chief goddess herself. The apostle is a playable character late in the game, and the true apostle (as this is a hereditary thing in this game and it turns out that the person believed to be the apostle wasn't the first-born after all) is one of the main characters. So yeah, I'm pretty sure that this actually works.
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[NO BARKLEY NO PEACE]