It's a bit silly of Spock to conclude that just because Mitchell's abilities grow exponentially they will eventually be infinite. So what if he's superior to you now, Spock, and continues to get better? That doesn't automatically and categorically make him infinitely powerful
Considering the evolution of Mitchell's powers (from speed reading, to mind reading, telekinisis, offensive lightning, matter creation), Spock was correct early on. It was too clear where Mitchell was going, so why assume limits?
But if he could easily make the ship blow up or crash, how could he be stopped? Hitting him with a fist would be the least likely way to succeed!
Kirk used his fists when Mitchell was rendered human
again--that was his best chance in a physical confrontation. If you notice, when GM was in "god" mode, Kirk used the most powerful personal weapon avaliable at the time.
Further, he already told doctor Piper what to do if he (Kirk) did not return, so the radiation option was always on the table. Meanwhile, Kirk was on a mission to not only kill GM, but to rescue Dehner--assumed to be normal, since he did not witness the transformation.