Actually, I’ll bet y’all are right. Betcha John Harrison is Johnny from ST(09). In fact, that makes extra JJ-sense what with him trying to cast Benicio del Toro or whomever for the role. He saw a coincidence, Johnny from the first film then remembered Mr. Harrison from TOS and saw a golden opportunity for a fanboy mindfrak, if you’ll pardon the expression.
It could well be that they had someone else in mind as the villain when they were trying to cast Benicio del Toro. I don't think the identity of the villain is as important as what has happened to him in the past few years, what made him who he is today. It doesn't matter if it's Lt. Harrison or Johnny, it only matters what became of them!