No, Scotty disabled a ship of the line [Excelsior], reducing it's effective and Starfleet's combat effectiveness.
KIRK: The Excelsior, ready for trial runs.
Scotty did not reduce Starfleet's combat effectiveness as the Excelsior was not in service.
And if Starfleet was canning everyone who disobeyed a direct order, Spock would be out already in S2E1 by your standards. So TOS and SNW apparently has that in common 
