-Staying to fight the cloud (Obsession)
Don't recall him disobeying orders on that one... I'll have to go back and rewatch it.
But, that said... the point of the episode was "Obsession" after all. This wasn't "the Kirk we usually see." He was, in other words, acting out-of-character.
-Searching for the Galileo (The Galileo Seven)
He wasn't dealing with chain-of-command, he was dealing with a bureaucrat, first off... and Kirk always chafed under those circumstances.
To use a contemporary parellel, it's like having a naval commanding officer react poorly to an order given to him by Barney Frank. Not "really" the same as reacting poorly to one given to him by the Secretary of the Navy. Even if Barney Frank has some form of "outside of the chain of command" authority in that particular situation.
Secondly, though... Kirk DID stay within the "letter of the law" in how he reacted. Yeah, he pushed it as far as he could, but he didn't cross the actual "line."
-Going back to the Asteroid Planet to save McCoy (For the World is Hollow..)
Haven't seen that one in years... but again, I'm not sure I recall the bit about him being ordered not to go back. Even if he was, that order really seems sort of nonsensical from a military standpoint (and hence would be an example of poor scriptwriting... which would carry through the rest of the script to one degree or another).
Supposing that Kirk was ordered not to fly back the few hours away in order to recover his trained Starfleet Officer CMO... well, that seems a bit odd. But I don't really care for this ep too much, so it's certainly possible that this is another flaw in what I see as a flawed ep anyway.
-Negotiating with the Ground Dwellers (The Cloud Minders)
Oh, good lord... definitely an episode best left forgotten (the sole high point being Droxine's dress...). I'm sure that Kirk got an order from some civilian authority to stop doing whatever he was doing. But again... "chain of command" means something different than "civilian authority." Kirk's situation put him under BOTH on occasion... but as far as I can recall, he only really chafed under the CIVILIAN authority, not the military chain-of-command.