Part of some of the anxieties felt at the making of Khan as the main villain of Into Darkness are self-inflicted. I agree with Nob that the villain didn't have to be Khan. Harrison worked just fine, or heck, he could've been one of the other crew of the Botany Bay (McPherson perhaps?) and cast Cumberbatch easily, no problem. But since they went the Khan route I think they should've cast a nonwhite actor. I think Khan is popular enough name/brand/character, if not his actual story, that it trumps him being a run of the mill brown skinned terrorist.
Plus Khan being a villain with some positive traits might have also undermined the dehumanized stereotype. Perhaps having a person of color back as Khan might dredge up those kind of vile feelings, but it might also present an intelligent, formidable brown skinned person that fans can possibly admire and understand. That might have changed perceptions in a way of turning Khan into a white guy, which avoids the issue, have not done. Taking on and confronting thorny issues is something Trek has a reputation for. Granted it is a reputation not always deserved, or as laudable as many of us wish it to be, but there's still a tradition there. Into Darkness did address some contemporary issues but dropped the ball in the casting of Khan.
I can understand your concerns about the casting of Khan back in the day. The skin darkening thing reminded me a bit too much of blackface and I have to wonder if Nicholas Meyer and/or Ricardo Montalban, etc. didn't think skin darkening would fly so easily by the 1980s as it did in the '60s.
I don't mind the idea of Khan being a challenge to white male dominance. I would rather that than for him to be a doormat or wall paper. And I think the idea of him being a kind of dangerous Other threat is somewhat offset by his intelligence, charm, charisma, concern for his crew, and enlightened despotism that even some of the Enterprise crew can sort of admire. As for McGivers it isn't a situation where he forces himself on her, he seduces her in part because she wants to be seduced. And his love for her and grief drive help drive him to madness in TWOK. So she was more than a plaything for him.