We now Harrison is working for Starfleet ...
We do? For certain?
Has their been an actual confirmation of this from someone actually involved in the production?
I hope you're not basing that on Peter Weller's line in the trailer that refers to "one of our top agents" being responsible, because that's most likely referring to Noel Clarke's character, whom Harrison recruits in exchange for saving the life of the man's daughter.
If you're basing it on images of Cumberbatch wearing a partial Starfleet uniform... why? Didn't the original Khan also briefly wear one in "Space Seed", even though he most certainly wasn't working for Starfleet? Ditto, that non-Starfleet 20th Century Air Force pilot they had to beam aboard in "Tomorrow is Yesterday"? And the android Norman from "I, Mudd"?
I'll put my answer in spoilers, just in case, but --
That is correct, he works for Starfleet as an agent of some sort. he does not hide the fact that he is the one getting his 'vengeance' so to speak. The questions are, why does he work for Starfleet and how long. The why may be that he is forced to, or has been secret all along and needs to be in Starfleet for some reason that fits his plans. It does feel that someone(s) in Starfleet was trying to use him and it backfired on them. We have seen so many movies and shows where an organization had tried to control something or someone more powerful then they are only to have it backfire on them. I think his reasons (if Kahn) is that someone is holding his augment brothers captives (Starfleet or the Klingons) and he is seeking to free them or even avenge them if they died.
Starfleet could have even had Kahns memory's suppressed and created the persona of Harrison. Then Kahn starts to remember who is actually is and starts his vengeance. so many possibilities...