Optimistically it was a happy ending. No more Comstock, so things are back to "normal". The thing I hate with these endings is that you never have any idea how much they remember. Whether Booker, whatever version survived (if he survived and its not just another hallucination like those occasional moments when he, the Luteces and Elizabeth were back in his PI office), remembers everything, or he just is suddenly worried about his daughter... and even then, Booker was seriously messed up after Wounded Knee and his time as a Pinkerton agent. But still, its better for the world if he just wallows in his despair rather than become a religious fanatic who has a superweapon at their disposal.
Really, I think it comes down to a... what was it, a grandfather paradox? If someone goes back in time and kills their own grandfather, then they're never born... but then if they never existed, who went back and killed the grandfather? Depending on the "rules" of whichever sci-fi universe it usually works out, but as seen at the end, almost any and everything has happened, is happening and will happen.
On a darker note, at the end, once Booker understood what was going on (not that Booker was ever stupid, just that this kind of stuff is way outside a normal person's knowledge, especially a supposedly normal early 1900 person), he did basically say to smother Comstock in his crib... probably being he is Comstock so, yeah. Symbolically any version of Comstock was born (again) at that baptism post-Wounded Knee, but hard to tell if any version of Booker survived, or any version of Elizabeth. Well, if a Booker and Anna survived guess that's still a happy ending, and the journey was definitely worth it.
