Funny, when I saw the thread title I had something else in mind.
But Wesley's "Jim, what are you doing?" is indeed rather odd, since Kirk says at the end of the episode that he knew
So it's safe to assume that this is mutual and Bob Wesley should know
that Kirk wasn't deliberately killing hundreds of fellow Starfleet crew members just because Wesley upsetted him by calling him "Captain Dunsel" (add to this he would have focused his revenge on the Lexington
Where the Wesley character confused me, too, was that he was apparently eager to eliminate the profession of starship captain / commander. Probably he wouldn't like to serve under the command of a computer, either and one may wonder how an M-5 would have resolved the situation in the TAS episode where the life of Wesley and his daughter were threatened.