The ending clearly shows that when Booker dies, eveything gets erased, which is quite wrong, as in the multiverse theory, what is done is done and there is no changing the present. Killing Booker just prevents a lot of the "Future" events, BUT.
If said future event already happened, there can be no way of erasing them. Croney Elizabeth ended a fair few worlds and in those timelines, well, it already happened. In order to really end it all, she should've invited Booker directly into the Past world that was affected and kill him then. All of the Bookers in fact, as every choice he makes creates an alternate universe, so there is a looooot of work to do to bring every Bookers into every root and kill them there and then.
Now that I think of it, affecting the future by altering the past is basically impossible. So yeah, Bioshock Infinite did the multiple worlds a bit clumsily.