I think that McCoy is a valued sounding board. And as Captain, Kirk needs to hear from various sources in order to make those important decisions.
I remember in the ep "Corbomite Maneuver" Kirk was not happy when McCoy questioned his decision regarding Bailey
MCCOY: Well, then about Bailey. Let me enter it in my medical records as simple fatigue.
KIRK: That's my decision, Doctor.
MCCOY: And your mistake. You overworked him, pushed him, expected too much from him.
KIRK: I'm ordering you to drop it. I have no time for you, your theories, your quaint philosophies.
MCCOY: I intend to challenge your actions in my records. I'll state that I warned you about Bailey's condition. Now that's no bluff.
KIRK: Any time you can bluff me, Doctor.
BALOK [OC]: Three minutes.
KIRK: All right, Doctor. Let's hope we have time to argue about it. Not chess, Mister Spock, poker. Do you know the game? Ship to ship.
UHURA: Hailing frequencies open, sir.
KIRK: This is the Captain of the Enterprise. Our respect for other lifeforms requires that we give you this warning. One critical item of information that has never been incorporated into the memory banks of any Earth ship. Since the early years of space exploration, Earth vessels have had incorporated into them a substance known as corbomite. It is a material and a device which prevents attack on us. If any destructive energy touches our vessel, a reverse reaction of equal strength is created, destroying
BALOK [OC]: You now have two minutes.
KIRK: Destroying the attacker! It may interest you to know that since the initial use of corbomite more than two of our centuries ago, no attacking vessel has survived the attempt. Death has little meaning to us. If it has none to you then attack us now. We grow annoyed at your foolishness.
SPOCK: However, it was well played. I regret not having learned more about this Balok. In some manner he was reminiscent of my father.
SCOTT: Then may heaven have helped your mother.
SPOCK: Quite the contrary. She considered herself a very fortunate Earth woman.
KIRK: Doc. Sorry.
MCCOY: For having other things on your mind? My fault. I don't how the devil you keep from punching me in the face.