See, that's what always confused me about that last scene. On the one hand we have the fairly clear order from Starfleet Command ordering the Enterprise to spacedock to be decomissioned. Yet, in his last log entry, Kirk says "This ship and her history will shortly become the care of another crew." Which seems clear that he is talking about another crew on the 1701-A. If he'd just said "This ship's history will become the care of another crew..." I could understand, but the two statements in the same scene seem at odds with each other. I'd really like to know what TPTB were thinking with that...
It was an awkward Next Generation reference. Supposedly the STVI writers were so clueless about Star Trek lore (and if you've read Denny Martin Flynn's follow-up novel The Fearful Summons
you'll have little trouble believing this) that they originally planned an ending where the Enterprise was handed over to Captain Picard and the Next Generation crew.
Recall also that "Yesterday's Enterprise" has already established the Klingon/Federation peace beginning 22 years prior to TNG with the sacrifice of the Enterprise-C. STVI ignored this. It also made McCoy and Uhura deeply incompetent, Kirk into a racist and Spock into a mind rapist. While also introducing a Klingon ability to fire while cloaked which they.... never bothered to try again.
IMO, STVI is a deeply