I agree, a fine scene. And it contrasts nicely with McCoy chastising Kirk in the previous film:
KIRK: Make your point, Doctor.
McCOY: The point, Captain, is that it's you who's competing. ...You rammed getting this command down Starfleet's throat. You've used this emergency to get Enterprise back.
KIRK: And I intend to keep her, is it that what you're saying?
McCOY: Yes! It's an obsession, an obsession that can blind you to far more immediate, and critical responsibilities.
And then in TWOK McCoy is urging Kirk to get his command back, rather than not pursuing it.
I know, different circumstances and such, but I think the scenes play well against each other.