I agree with your criticism of the way Starfleet is depicted. I remember reading a fanzine article on the movie, where it brought that issue up, saying essentially "what the heck has happened to Starfleet?"
Actually, the whole subplot of the "going renegade" against Starfleet has always seemed very contrived to me. I mean, Kirk was THERE at the formation of the Genesis planet, and he's an admiral, and one of the most famous figures in the Federation. Yet Starfleet is throwing up all these bureaucratic obstacles in his path for no reason other than to create conflict.
I don't know. Kirk butting heads with the brass and Federation bureaucrats was kind of a staple of the original series. Kirk defied orders to divert course to Vulcan in "Amok Time," for instance. And he regularly clashed with troublesome Commissioners in episodes like "The Trouble with Tribbles," "A Taste of Armageddon," "The Galileo Seven," etc.
This was the same sorta thing, just on a larger scale.