Ok, so the ending is a play on the multiverese theory from quantum phisics, where every possible combination of an event, actually happens. For example we could have a parallel universe in which the roman empire never falls, Alexander the great never defeats Darius, etc. But it intoduces something new: constants. There will allways be a lighthouse, a city, a man with an idea, a girl, some guy to bring it all down, a scientist, etc...
So, at the point of the baptism, whatever Dewitt choses, in at least several universes he becomes Comstock and builds Columbia, in others, he joins the Pinkerton's and ,at least in one, he never goes to the baptism in the first place (the Anna that doesn't dissappear). Now, by killing Dewitt, you're destroying Columbia, but you're forgetting the constants. Another one will have to take Comstock's place and build a dystopia (''There is allways a lighthouse, there's allways a man, there's allways a city...''). You're not just taking the card out of the deck, you're also reshuffling the deck. So, basically, you're killing yourself on the chance that the guy replacing Comstock and builds the utopia, fares better than the prophet.
But the chance of that happening seems very slim. So far, the track record for utopias that stay utopias is very crappy: Columbia was a heaven of racism and slavery, that comes crashing down or tries to enslave the world, Rapture turned its people into crazy murdering junkies. Who's to say that some other nut doesn't come along and starts the 2nd holocaust? You could say that in every universe where Comstock exists, millions die. Millions will die anyway: if it's not the inquisition it's the plague, if it's not the plague it's the crusaddes, if not the crusades then the world wars, etc.. Just because you stop one of these doesn't mean that the next one doesn't appear or that another one doesn't take it's place. So the suicide seems kinda pointless. Either way a new city is build and you're grasping straws that maybe it will be better. If it's not Rapture it's Columbia, if it's not Columbia it's ............ (insert name of city from sequal :D )
Maybe I'm looking at it the wrong way, but from this angle the ending kinda feels even emptier. IMO, either way, the ending falls flat and emotionless. The entire game is filled with emotion, and attachement to the 2 characters. But in the end, everything is reduced to an equation of quantum physics. Seems kinda 'meh''. Plus, the post credits scene is a bit too ''Inceptionesque''.