So far I've found the generally accepted interpretation of the the ending is that Elizabeth prevents Comstock from ever existing by having him drown at the baptism. And I agree, this seems to be the intended interpretation considering all the talk leading up to the final lighthouse and the fact that the various Elizabeths disappear at the end. But the implications of that ending are actually pretty fucked up.
You're not just eliminating Comstock. We see all the Elizabeths at the baptism disappear as well. But it wouldn't just end with her, would it? No, you're eliminating everybody in those dimensions where Comstock exists. Everybody. Those people that Elizabeth danced with on Battleship Bay -- gone. That little kid hiding under the stairs who she sang to and fed an apple -- gone. Everybody. "He is alive in a million million worlds." That's a million million everybodys -- gone.
It kinda turns Elizabeth into a petty, vengeful god. Sure it sucks that in some dimensions Comstock tortures and indoctrinates her, but that doesn't make Comstock so overwhelmingly evil that his nonexistence is worth the sacrifice of all those people living in those dimensions. So Columbia might wage war on the the world below. That sucks for some folks, but (Godwin's Law Warning: Begin rolling eyes now) if she was a Holocaust victim, would she be justified in eliminating all of us because we live in a world where Hitler rose to power and World War II happened? Is it even necessary to end the story with such a literal and absolute defeat of Comstock? I don't think it is.
I think Elizabeth gaining omniscience over the multiverse is enough of a resolution. Didn't she really just want to know the truth? She doesn't need to beat Comstock by snuffing out the possibility of his existence because she can see his insignificance in the grand scheme of things now. His dimensions, even in their millions, are just a drop of guppy shit in the ocean of the multiverse. I'd prefer it if Elizabeth showed a little more tact considering her enlightened perspective on things. It would be a better ending to that conflict.
To me, the final baptism is only closure to the personal story between Booker and Elizabeth. They don't drown him, they just submerge him and transport him to the post-credits scene. The baptism is meant to be a symbolic gesture of forgiveness made genuine by the way it differs from Comstock's baptism.
God in this case is actually Elizabeth, who is now omniscient. And the baptism is performed by the various iterations of her rather than some random preacher. On one level the scene is about Elizabeth, the person(s) Booker betrayed and sold, forgiving him by appearing at and performing the baptism. Where the preacher talks about erasing the past, the Elizabeths do the opposite. They simply say "He's Zachary Comstock" and "He's Booker DeWitt" to which he replies "I'm both". This baptism is about owning his sins rather than erasing them. And on another level it's about Elizabeth the quasi-god. She sees everything Booker can be and gives our version of him another chance with Anna, as an act of grace.
I feel like this interpretation is more consistent with Elizabeth's character. No need to drown or delete anybody. Don't ask me why the Elizabeths disappear at the end. Maybe they teleport to Paris or something.