It's pretty clear from the TMP film, novelization, and The Lost Years
that Kirk was rather powerless to do much of anything about such a drastic redesign of the Enterprise
following its return from the five-year mission -- Starfleet was hell-bent upon the refit program, and Kirk suddenly became far too valuable a commodity as a returning hero and as a recently-promoted Admiral (the new public "face" of Starfleet) to have any real impact against the decision.
He certainly hoped
to regain a say in the proceedings -- he only accepted the promotion to the Admiralty on a provisional basis after nearly tendering his resignation, but soon found himself too embroiled in other duties as Chief of Starfleet Operations (and roving diplomatic troubleshooter) to involve himself in the refit process.
Plus, Decker had already been promoted and was overseeing the entire program by this point, and it basically took the intervention of Admiral Nogura himself years later to finally get Kirk his old command back (albeit much too late to prevent the refit).