Because of the altered timeline, pretty much all of the history is suspect, but we do know that everything prior to Kirk's birth would have to be the same as that is when the timeline split off (unless Spock was running around mucking with the timeline before the Romulans came through, which I highly doubt). So we do know that the Botany Bay would have been out there somewhere, seeing as it and the eugenics war happened prior to the time split.
I do think that from the movie maker's standpoint, if they were going to tie it in any way to the original Botany Bay storyline, they would never include that and not include Kahn. The fan reaction would just be too extreme if they included the augments and not have Kahn.
What I'm really interested in seeing though (and I hope they do expand on it) is how the Vulcan empire is going to react to their homeworld being destroyed.
