Something I don't get/rubs me the wrong way:
Comstock had to die at his birth to prevent everything from happening. Why then, is the Booker who did not accept the baptism (the one you're playing as) killed? All the Elizabeth's disappeared, again indicating that the "good" Booker was killed because the "bad" one who created Columbia is sterile.
It's just kind of fucked up that the Booker who is a father dies, and the evil dictator lives (but doesn't get a heir to the throne, presumably). I hope I'm wrong.