Kirk could also have known there was "no life" aboard the Excalibur because he knew full well all the surviving crew would've already abandoned ship by the time he asks M-5 the question.
Remember, not only does Kirk know what the Enterprise weapons can do, but one can presume he knows all abandon ship procedures and timetables for a Constitution class starship.
Remember, Kirk also asks M-5 what the penalty is for "murder". M-5 replies "death".
We know from "The Menagerie" that going to Talos IV is the "only death penalty still on the books".
So if M-5 were being the least bit reasonable when Kirk asked what the penalty for murder was, M-5 should've replied
"Lifetime incarceration in a Federation rehabilitation facility" or something that effect.