McCoy was always written as the odd one out: "I'm just an old country doctor", and such. Even more so nowadays. In modern stortelling, the moral, sensitive, confrontational side of the "power trio" is almost always female. Whether or not Zoe Saldana's Uhurra gets promoted to second lead (its plausible!), or McCoy demoted to comic relief, all depends on how they treat these characters in future films.
Encouragingly, this movie was all about giving each person a moment in the spotlight, something all the best Trek movies have tried to do. McCoy's just happened to have a funnier one ("I've never seen a reaction this severe since med school!" - "Damn it Jim, hold still!").
But then again... Zoe Saldana can carry her own movie at this point, right? I'm not even sure Chris Pine has that star-power yet.
We may be looking at a "Storm<Cyclops-from-X-Men-3" sitaution here (for some Trekkies anyway). Halle Berry was a huge star, and James Marsden was just some asshole wearing a visor. As a result Cyclops, who played an essential role in the original comic (and during the Phoenix story arc, no less), got relegated to the background and then killed off ten minutes in. I don't think McCoy's at risk of the latter, but I'm just sayin: is that such a bad thing?