If you haven't played Burial at Sea, don't reveal the spoilers please.
One has to keep in mind that each choice made creates a new set of universes. This does not mean an either/or choice - as many universes/paths will diverge as there are options. Also, remember that each either/or choice always has not two, but actually three choices - there's the option to abstain from choosing. From there, choices explode (how was the choice bypassed? A clever line? An event? etc.).
It is also very worth noting that the only universes seemingly "erased" from existence were universes that dealt with Elisabeth being tortured/tormented in any way (thus giving her cause for correcting them). Other realities remain unaffected.
Of course, this can all be "waved away" by assuming that each subsequent choice is in fact - subsequent. As in, "you can change time, but you cannot change history". Consider: you eat a burger, you feel sick, you go back in time, you don't eat the burger. Time was changed, but history (cause - effect) still stands and chronicles what occured. You still didn't eat the burger because you felt sick after eating it previously - you didn't erase history by changing the past. (this theory is also known as the subjective timeflow theory)
This, of course, allows Elisabeth to continue existing. Her past torment is now gone, but she will still remember it.
(as she clearly does in Burial at Sea)
She didn't break the chain to stop herself from being tortured - she meant to void the entire phenomena set, so that it wouldn't perpetuate any further, and no more lives would be affected as hers was.
Of course, there's another massive hole in the plot - Burial at Sea itself, or how did Comstock escape to Rapture when all realities related to his existence at all were erased? But that's a different story altogether.