I don't know... Putting aside the whole argument about Uhura and McCoy in terms of their place in this new universe and whether it's justified or what have you, I do think from a character standpoint it would have been nice to have Bones there. Remember, McCoy and Kirk were friends for several years before either of them even met Spock.
He could have called back to his own remarks at the beginning of the movie with regards to saving Spock. Scotty could stop McCoy from trying to open the hatch and save Kirk. "We can't just let him die!" "You're not going in there, Doctor! You'll kill us all."