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.
Nah. Not buying that.
Too much is being made of Kirk telling the M-5 tie-in "because you murdered it!"
It is not necessary for the M-5's attack on the Excalibur to have killed the entire crew in order for Kirk's moral plea to carry weight. The dialogue between Kirk and the M-5 tie-in was simply dramatic short-hand that M-5's attack killed people, period. It didn't have to kill all 400+ (although that does work dramatically in that scene), just that the attack cost lives rather than saved them. Earlier in the episode Dr. Daystom laments this point:
MCCOY: Have you found a solution, a way to shut that thing off?
DAYSTROM: You don't shut a child off when it makes a mistake. M-5 is growing, learning.
MCCOY: Learning to kill!
DAYSTROM: To defend itself! Quite a different thing! When a child is taught, it's programmed with simple instructions, and at some point, if its mind develops properly, it exceeds the sum of what it was taught, thinks independently.
MCCOY: That thing is a danger to us all. Now find some way to shut it off.
DAYSTROM: You can't understand! You're frightened because you can't understand! I'm going to show you! I'm going to show all of you! It takes four hundred thirty people to man a starship. With this, you don't need anyone! One machine can do all those things they send men out to do now. Men no longer need die in space or on some alien world! Men can live and go on to achieve greater things than fact-finding and dying for galactic space, which is neither ours to give or to take! They can't understand. We don't want to destroy life, we want to save it!
It seems from this scene that Daystrom believed his creation would save lives by making astronauts either obsolete or mostly supplanted by AI-driven space travel. McCoy had to share this with Kirk (we see at least part of their conversation in the briefing room; there was likely more on their way to meet Spock and Scott in the Jefferies Tube) because McCoy recognized that the conversation in the Engine Room gave him insight into Daystrom's p.o.v.
Subsequently, when Kirk confronted the M-5 tie-in that M-5's war-on-Wesley's-Task-Force was resulting in the loss of lives, it shouldn't matter whether it was 40 or 400. Murder is murder. That's what Kirk impressed on the "Ultimate Computer". Obviously, Kirk was appealing to Daystrom's (implied) prime directive: "Men can live and go on to achieve greater things than fact-finding and dying for galactic space, which is neither ours to give or to take... ... We don't want to destroy life, we want to save it!"
When Kirk confronted the M-5 tie-in with this dilemma, M-5 realized that it had defeated its own "purpose in life" and witness the result:
KIRK: And how will you pay for your acts of murder?
M5 TIE-IN: This... unit... must... die.
My reasoning in pointing out the Enterprise crew's brighter mood prior to setting course for the space station (instead of mourning the loss of an entire sistership's crew) was that (1: obviously some time had passed between Wesley giving the cease-fire order over the radio and McCoy's report to Kirk on Daystrom's condition in Sickbay, clearly spelled out using the starship visual as a "fragmentation of time" device implying "later..."; and (2: nobody seems bitter or sad; they actually seem relieved and upbeat, which suggests to me that the M-5 war-games disaster did have a silver lining: at least some of the Excalibur crew survived and were rescued, possibly transferred to the Enterprise. (this would explain how the ship could make it back to the space station without M-5's help)