Probably because we don't actually know what happened. MC isn't exactly in the state of mind to confront what he has blocked off in order to cope....how can he possibly utilize her operationally. I still don't see why he feels so much guilt for dude getting fragged in the first place to the point that he'd even possibly consider helping her get elected. PTSD I totally get, but dunno that scene should have played out much differently in my opinion and was the only time in the game I felt railroaded.
And considering Safiya's background and status, along with the theme of both chapters, maybe realizing how ineffective the squad has been and ill-fitted to take charge of these type of operations are; It is probably part of MC's trial to work it all out.