Pike isn't/didn't ignore M'Benga's confession. Pike is evakluatging it in context of everything surrounding it. Yes, the 'Letter' of Federation Law and Star Fleet regulations would see M'Benga prosecuted and imprisioned for it BUT:
- Pike understands that Dak'Rah was a war criminal, as weel as a traitor to his own people and Starfleet and the Federation themselves are IGNORING that aspect of his past because he serves a useful purpose. (Remember that Star Fleet sent a Special Operations team to kill Dak'Rah becausae of his actions and the Brass hoped M'Benga would participate, but he didn't and that mission failed.
- Pike sees that the Klingon Empire wanted Dak'Rah dead for being a traitor; and the Klingon Empire wasn't sending its soldiers after M'Benga for any retribution - rather Dak'Rah's own daughter is wanting to engage and kill M'Benga because her Klingon Family's Honor has been destroyed, and by the Klingon's Honor Code to erestore it she eother had kill Dak'Rah herself OR killm the person who actually killed Dak'Rah.
Pike knows M'Benga's service history, so he understands and accepts what M'Benga did in SNW S2 E8 Under The Cloak Of War. Hell, I believe Pike trhought M'Benga did decide to and killed Dak'Rah when Dak'Rah himself confrnted M'Benga the way he did. Remeber M'Benga didn't just launch into a rage and murder Dak'Rah; M'Benga gave that Klingon a couple of chances to walk away before Dak'Rah effectively threw himself at M'Benga. There was also the fact that Dak'Rah SAW that Dr. M'Benga had kept the knife that Dak'Rah had left behind (but Dak'Rah had never told anuyone that); and realized M'Benga could wreck Dak'Rah's Federation career IF M'Benga revealed that fact and the knife was anallyzed.
(IE - I'll posit that Dak'Rah, once he knew the above was either going to get M'Benga to join him as his partner in the diplomatic core OR failing that get and allow M'Benga to murder him as Dak'Rah himself realized he waqs too much a coward and could bring himself to commit suicide; so yeah, M'Benga was Dak'Rah's own too for effectively killing himself.)
I don't believe Pike ever felt that waht M'Benga did was morally ambiguous - M'Benga was in a way forced to finish a personal (and sanctioned) mission he took upon himself during teh Federation/Klingon War once he waqs effectively offered the chance to do so.
JJ Kirk's actions againt Nero's crew in ST09 aren't morally ambigous either. Nero and his crew WILLFULLY destryed the planet Vulcan itself and killed every Vulcan still on it. (They also killed the crews of an entire Klingon Fleet - but again, I doult the Star Fleet Admiralty would shed a tear for that action.)
^^^
So again, I've no problem with cheering Kirk on as Nero deserved what he got as did the crew who willfully followed a illegal and genocidal order.
So JJ Kirk is no different than prime Kirk (who if he didn't have Spock beside him or bailing him out of some really crazy ideas and plane he undertook, would have been dead or sutting court martialed in a Federation prison before the successful end of his original 5 year mission.)
M'Benga's trugthful confession would be enough IF he he gave it in a Court of Federation law; which he might have done (since he is still conflicted about it himself); and probably woujld be put before such a Court IF Pike ever reported said confession to Star Fleet and Federation authorities; but that isn't going to happen as Pike said what he would report (if he made one) was that he saw his friend LIE tom a Klingon soldier to save Pike's life as said Klingon WAS holding a knife to his throat and the only way she would let P{ike go is if M'Benga admitted to killing Dak'Rah and fought her in ritual combat.