True, I don't have an encyclopedic memory or anything of the show, but it does seem like often times there were discussions of it taking weeks or longer for messages to get to Starfleet Command and back, therefore Kirk had to make his decisions with no guidance from his superiors.
Kirk, Spock, and the original crew were also time travelers:
operating outside the reach of Starfleet, going where no man had gone before. Starfleet could not follow, track, or control them. They were pioneers truly going where no man had gone before.