I don't see this as remotely similar to those other situations. Dealing with some self-important politico operating well out of his comfort level is nothing like the overall feel of coming back to an Earth where, as my favorite 90s era commander would say, 'nothing's the same anymore.' The stakes of Kirk losing his command were the same in many eps as SFS, but that kind of thing is just a go-to for kicking things up a notch dramatically, whereas the situation in SFS suggests something much further reaching and dire (probably not unlike the stuff in the first Shatnerverse book, which I recall as having a guy something like the Peter Weller character in the new movie.)
Even the defying-Starfleet-on-getting-Spock-to-Vulcan thing is a matter of a commander in the field making the on-the-spot call, which can be justified to some degree even w/o T'Pau's assistance. I think I remember David Gerrold's assessment of the way things were in SFS in his revised WORLD OF STAR TREK -- the one I didn't ever buy because it cut too much good stuff from the original -- was that it looks like Starfleet doesn't ever want this team operating together again, so it wasn't just me getting that vibe from the movie. Whether that is just the Bennettization of Trek or something else, I don't know, but it felt as wrong and unTrek to me as seeing the blocky ILM-designed structure that lacked the built-in-space beauty of the TMP latticework dock.
I've only rarely ever gotten out of a movie and went home to write what I thought the followup had to be -- it happened with ALIENS and with SFS. Neither of them remotely resembled what the followups actually were (my aliens followup was probably closer to what the next PROMETHEUS sequel might be in terms of where they went, but not what they did), but in the case of SFS, I really thought Kirk & co needed to spend their golden years doing their thing on their own, that the whole Starfleet/Federation aspect was a big weight on the storytelling as well as being an expense to have to depict which could be saved and put into depicting those strange new worlds in ways that didn't look like white blankets on top of inverted tripods (which is how some of those cacti look in SFS.)
Plus I felt then (and still do) that I was a lot more interested in these people than in the organization they served as depicted in the films
. Would have been very happy to see these folks FIREFLYing along in the BoP for another few pics. I remember my mom liking the idea as a way of getting back to ShangriLa, or 'you CAN go home again, you just can't take the old familiar family car to get there.'