While I agree that Scott and Kirk didn't seem like they were bluffing I can't see Scotty just wiping out an entire half-planet of whatever they could of the major planetary cities in range without Kirk's reconfirmation or Spock's.
Scott will understand that Kirk is the King of the Bluffs and may be going along withe the bluff. After all Scott would only need wipe out a couple of cities for them to pay attention.
However Kirk was considering killing all the Denevians so he obviously has the authority to carry out mass murder. At this episode in TOS maybe Kirk has to show that the Federation is not to be missed with.