So, a thing about fantasy (genre fiction in general, really) is that good fantasy requires the protagonist to be the center of the conflict. The higher the stakes of the story, the more necessary this becomes. You can't write a saving-the-world plot about some dirt farmer who dies of cholera while the real main characters are off-screen doing the saving the world part. I mean, you could, but it'd be really frustrating. So any good fantasy protagonist is going to be a Mary Sue to at least some extent: The author has to contrive a reason why this person serves as the fulcrum, and that's necessarily gonna be a contrivance. It's just something you have to learn to swallow if you're going to enjoy fantasy fiction at all. (And some people don't enjoy fantasy for precisely this reason, and that's okay.)
And, come *on*, collecting a harem is a self-indulgent Mary Sue trait all on its own.
That said, there is such a thing as layering on *too much* specialness. A protagonist should be as Special as they need to be to justify the plot turning upon them and their decisions: Anything more than that is simply excessive. A common newbie mistake is to make the protagonist a lost prince who must reclaim his throne from his evil uncle... and then also make him half-dragon, and the reincarnation of an ancient archwizard, and have him find a sword that once slew a god, and also make his eyes shift in rainbow colors just because that looks cool, etc. etc. etc.
I think, in Ataegina's case, the hero having the Father inside of him is more than enough. Making him *also* the reincarnation of the Good God is definitely excessive. But ah well, there's far, far worse sins a story can have, in my opinion, and so long as the author is having fun with it I don't really care.
