I honestly think that Into Darkness would have been a better movie (and certainly better received) if John Harrison had just been John Harrison....and Khan had still been a Popsicle.
Personally, I liked the idea that Harrison was just another one of Khan's people in cryofreeze, and the real Khan is still there sleeping.... they were all super intelligent ruling elite supermen... not just Khan! Although I definitely like the idea that Khan/Harrison could have been redeemed or helpful, considering his descent into totally villiany happened after being stranded on a dead planet for so long.