It should be noted that ST6 does not exactly indicate a change in the ship's status yet. True, Uhura receives a message saying that "they" are to be decommissioned, yet Kirk responds with a log entry that refers to the ongoing mission of this very vessel under future crews.
OTOH, we already knew that "they", as in our heroic officers, were to be retired very soon...
Perhaps Starfleet revokes the commissions of all its retiring officers? Or perhaps revoking of commission was to be punishment for Kirk and his team (although apparently not followed through since the heroes still have their uniforms in ST:GEN).
The decision not to repair the ship would then come later, supporting the theories of political pressure and downplaying those relating to Starfleet's original plans on the ship or the class.