Honestly i always thought the same thing. Why couldn't they have given him one measley line to make him seem more 'with-it.'
"Jim, if M-5 is out of control you have to disable it quick or we'll be forced to destroy the enterprise!"
Two reasons why this line would have been pointless.
Enterprise couldn't respond and I think Wesley was feed so much information about how frikkin' wonderful M-5 was that this never even entered his thought process. Kirk said the government bought it and they were going to make it work. And being a Commodore, Wesley's personal job of ordering ships around probably wasn't in jeopardy, just the captains under him, which he didn't show too much sympathy for, did he?
Really, how often do you expect your new car to turn on you and attack? It's supposed to be a new computer, they're up to their asses in computers, why would one turn into a crazy kill box? And Daystrom himself is on the ship with the M-5, if there were any problems, surely he would take care of it? Right?
I don't think anyone planned for M-5 to suck the energy out of the warp engines like a slurpy, so any previous manual overides were useless. How does one manually control a starship, do you mean there are actual sticks and cables to fly it?
Sorry if I'm posting short, I'm not trying to be nasty, I just think it would have been the farthest thing from his mind, he was basically in the position of having an out of control starship to deal with at that point, it had to be stopped whoever was in control.