I like this theory but now that I look at the actual dialog, it sounds a bit contradictory (the dialog, not the theory).
Captain, I have orders from Starfleet Command. We're to put back into Spacedock immediately, ...to be decommissioned.
Then Kirk's final log entry says this:
Captain's log, U.S.S. Enterprise, stardate 9529.1. This is the final cruise of the Starship Enterprise under my command. This ship and her history will shortly become the care of another crew. To them and their posterity will we commit our future. They will continue the voyages we have begun and journey to all the undiscovered countries, boldly going where no man, where no one, ...has gone before.
Uhura's statement makes it sound like the ship is being decommissioned (being put back into Spacedock), along with the senior staff. I don't know how the US Navy does it, but I've never heard of people being "decommissioned" from service. "Retired", "mustered out", "DD-214'd", yes, but not "decommissioned". I thought that term was reserved only for equipment.
But then Kirk says "This is the final cruise of the Starship Enterprise under my command. This ship and her history will shortly become the care of another crew.", what you were referring to, Tribble Puncher
I guess it could be legitimately argued that the E-A went on without Kirk & company, which would add to the impact of Spock's "go to hell" line. It's kind of a shitty thing to send out a broadcast message saying "guys, you're too old, get off our ship after you almost died saving the Federation from intergalactic war once again!" Then again, I guess this is what we can expect from an institution that openly advocated the highly unprofessional and uniquely demeaning concept of "Captain Dunsel".