Yes, I think this is most likely, too. Remember how Kirk's quick thinking saved Khan from a malfunctioning cryogenic chamber in "Space Seed?" What if a different starship (not Enterprise) encountered Botany Bay in the new timeline? What if Khan dies because the captain who finds him isn't as quick? What if, for that matter, the augments either overtake that unlucky starship--or lay low and quietly assimilate--before hatching a plan to wreak havoc once they have a better lay of the land? John Harrison is probably from the same group--but just nastier (and more successful) than Khan.