But then in that case Kirk wouldn't have asserted that the reason for there being no life was because the M5 had murdered it. You don't likely get a second chance to out-think a super smart machine.
That assumes that M5 would have been as well versed in Constitution
evacuation procedures as Kirk. But since it's a machine that's not supposed to have
any crew, Kirk might trust it would not stop to consider evacuation as a reason for the total loss of life at the ship it had targeted...
Considering M5 schooled Kirk on proper selection of a landing party and led Scotty and Spock on a wild goose chase on how to divert control of the ship it would be very safe to say that M5 is well versed in all things Constitution-class including evacuation procedures.
But as you point out, it's one weakness is that it has Daystrom's failings and that is what Kirk used against it. However, for Kirk's argument to work, M5 really needed to believe that it murdered the crew of the Excalibur and that would suggest that it indeed did so.