I think that the Other Person's post was certainly well thought out and definitely had its points, but completely left out one factor - taking responsibility for your actions.

Yes. That's precisely where it breaks down for me. The Atlanteans' treatment of Michael was bad, but it in no way does it excuse what he did afterward. Leaving him alive would be irresponsible. He's a psychopathic genius, and any non-violent solution that they could have come up with would've had far too much potential for him to escape and resume his program of genocide.

I did think about Miller's Crossing while I was writing the above. Personally I think that Wallace's death was a much greyer situation than Michael's, for a number of reasons -- the situations (the magnitude of the crimes committed; the culpability or lack thereof of the Atlanteans, etc) are not really all that comparable. I haven't really seen a whole lot of meta surrounding this episode, though -- I think that most fans are a) blinded by squee (not that I can blame them. :D) and b) not really conflicted over Michael's death in particular. (Which I'm not, either. :D)