I guess I will just have to disagree on every single item and interpretation above... Again.
Look, I'm not out to disprove that Kirk would be a starship captain. It says so in his resume, I suppose, even without having seen that. What seems clear from TOS and necessary in the context is that Kirk is not a special starship captain, and furthermore that a starship captain is not a particularly rare or special position in Starfleet, any more than a ship captain is a rare or special position in today's navies. I.e. it is not a special captaincy in Starfleet, it's merely a captaincy in Starfleet, which makes it special as far as captaincies go.
Stone already says that random people in Starfleet, such as commanders of starbases, may be starship captains. He then summons two further starship captains from the nearest bar (we saw them hanging around there shortly before the shit hit the fan) for Kirk's trial.
Starfleet simply is the place where one finds starship captains. And Kirk risks becoming a famous one for being the first to stand trial for something that could end up badly for him. Prior to that, he has no known claim to fame.
Merrick is a civilian pointing out that Kirk is military. Finney is sarcastic. And McCoy is just sprouting random psychoshit. None of this would offer any support for Kirk being special among his own kind, or indeed special in any fashion, if it weren't for the fact that Kirk is the hero of a rather exciting bit of 23rd century reality television.
Timo Saloniemi