I can agree about the symbolism of the faulty bio-bed at the end... although I don't think M'Benga had the presence of mind to interpret it with any sense of regret about the hollowness of revenge. His voiceover suggests that it's more just a matter of resignation that some things (including his sense of self) will stubbornly remain broken beyond fixing.
I can't remotely agree that Dak'Rah "had it coming." To me he came across not as "untrustworthy," but as someone who was sincerely trying to turn his life around and attempt to balance the scales for past acts (even if he allowed certain public myths about those past acts to persist). The entire Federation diplomatic corps presumably agreed with that judgment. You (or M'Benga) are free to disagree, of course, but at most that would warrant a trial with due process—it hardly justifies murder. (Nor, hopefully needless to say, does pestering someone who asks to be left alone.)
And that's what it was: murder. We have no evidence that it was self-defense (not least because the scene was (shamefully) shot to obscure the details), and the build-up certainly doesn't warrant that assumption.
I'll grant that perhaps it's not outright character assassination of M'Benga, if only because he has (admittedly limited) previous appearances in canon, although it is at least a distortion of his otherwise admirable and humanitarian character as seen in those instances, not to mention (several more) appearances in Trek "fiction." However, it is definitely character assassination of Chapel, who is not someone we have ever previously had reason to believe would let a person bleed out on the sickbay floor and then lie about it under oath.
Nor can I easily accept the rushed ending as a mere artifact of "one-episode structure," especially given how much (poorly paced) time was given to the flashbacks throughout the episode. It speaks poorly of Pike, Number One, and Spock that they would be so quick to sweep this under the rug, and poorly of Starfleet that it would let them do so. And I'm really starting to get tired of stories that paint a cynical portrait of Starfleet and its personnel (even our protagonists!) not living up to their ideals.