I really don't see any issue here at all. If anything, it's good that Uhura is finally getting her moment. Hell, for the first 42 years of the franchise she didn't have a first name and the only thing memorable she did was force a guy into a closet at gun point.
Giving her a more significant role is one of the few things Abrams is doing correct since he's finally developing an underdeveloped character and he's actually doing something unique with his Star Trek.
Yeah, we all love Bones and Karl Urban is great in the role, but so what if these movies have a different dynamic than TOS and its movies? Isn't the opportunity to do something different the reason to do a reboot?
Oh, sorry, forgot this is the forum that wants the the movie to be a remake of Space Seed/TWOK with Gary Mitchell somehow mixed in.