Infinite Realities = *Spoilers*
Elizabeth implied that there were an infinite number of realities (Hence the title of the game?).
So if you take say, half of them to be when Booker chose to be baptised and be Comstock, there would still be infinite realities where Booker becomes Comstock (since Infinite / 2 = Infinite)
Therefore there is no way of preventing Comstock from existing since you can't kill an infinite number of baptised Bookers from an infinite number of realities.
Also, if the idea was to prevent Booker's baptism, why not just go back further in time and prevent him from ever joining the US Army (And Wounded Knee massacre) in the first place? Or something along those lines?
IMO, Bioshock Infinite's ending is good (which sad, touching ending isn't?) but doesn't really make much sense.