I can't picture Khan working for Starfleet in any capacity.
My guess is that Harrison is one of Khan's people, pulled out of stasis early while Khan and the rest of them are still asleep in their chambers, being kept hidden away somewhere. Maybe he was in one of the chambers that failed in the prime universe before Enterprise found them, so he missed out on all that happened there. But in the alternate universe he was rescued, quickly escaped from his would-be masters, and is now wreaking havoc to find and wake up Khan and the others. So in that sense he is a new character, but also a canonical one. The Bad Robot crew gets to dive into Trek lore while still forging their own.
Or I could be completely wrong. Who knows. My butt will be in the seat regardless.