Okay, here's the thing, no matter who he is, they're not gonna make him some "only Trekkie's know him" character. That defeats the whole purpose of ditching the top heavy continuity. The more you overthink this, the more wrong your conclusion is going to be. Whoever he is, he has to be easily accessible to "Joe I. HateStarTrek." And some dude unconscious on the floor of the bridge in Space Seed ain't that guy.
He's either Khan, because everybody's grandmother knows Khan, or he's John Harrison, a new character they created for the movie.