Yeah I actually get the whole part about killing him before he makes the choice or creating a paradox to prevent the possibility of him accepting the baptism. The problem I have is wrapping my head around which Booker(s) get killed.
From my interpretation, all of them get killed and that is what creates the paradox. Most people seem convinced that it is an either/or question, but I would say that since we as a singular booker are seeing all the liz's from different realities, that makes that one Booker a constant. Clearly it is hard to say as there is no hard evidence if there even were Bookers who did not go to the baptism or any other variations.
Liz is not just reshuffling the variables, but removing a constant which in turn makes the universe collapse all realities, rewind and start new - effectively giving them all a new start.
The only thing that doesn't fully fit there is that Booker is so agitated when he wakes up, but I'm fine with accepting him adjusting to the new reality and still having the fading memory similar to what we all have after a nightmare. (makes one think, maybe it was all just a dream - dun dun dun!)
Ultimately, we as a player are the only constant observer to the whole thing and that would only leave our individual perception to be the defining anchor that everything wraps around one way or the other. That still makes it an infinite amount of universes depending on the number of players and playthroughs.
On an unrelated side note, I really like how character respawns were given a story explanation in Infinite and how it is literally the interactive version of the hero with a thousand faces that also is presented on a small enough scale for us to appreciate it from outside the box in its multitude.