I'm slowly coming around to the idea (advanced in another thread) that not only is Cumberbatch not Khan, but that it really doesn't matter who "John Harrison" even is. Storywise he's Darth Maul, General Grievous, Bane, the guy Robert Carlyle was playing in The World Is Not Enough.
In other words, he's a distraction. A red herring. A decoy. A henchman at best. The REAL bad guy (girl?) of Star Trek Into Darkness is someone we haven't met yet, someone the prerelease marketing isn't even hinting at.
I agree with you up to a point. I think Cumberbatch is not Khan but possibly one of his henchmen that got thawed out early and Khan will be in the next film.
This movie or the next have absolutely nothing to do with Khan whatsoever.