The timeline they went during the ending was the time when he was about to be baptised and killed that booker there, hence destroying what ever happened after that.
I think the world he rejected goes on as normal, but his debts doesn't show during the after credits, so you might be right on both worlds being destroyed. =/
There are a lot of constant and variables, so I guess the after credits was the rejected booker, but had a good life instead of having debts. Could be either way, but also in that constant will have a lighthouse, a crazy man, and a weird city.