The broad failure of human rights enforcement required for these events absolutely could not have happened over the objections of all, or even most, on the military side. Tacit and widespread approval of Washington's agenda on 'terrorism' was, at the very least, a precondition.
Taking this in context of his broader point: I can see why it would be comforting to believe institutional norms tend to be stronger than petty politics, but if that's the case he wants to make, I'm not convinced. To me, the preponderance of evidence, and the typical patterns that occur when a military attempts to circumvent democratic processes to 'safeguard rule of law', would indicate that military norms around human rights tend to break down, in fact, much quicker than the norms of democratic civil procedure. I also have no good reason to believe the US military is exceptionally ahead of the curve in this regard.
Could there be a situation where military intervention prevents a democratic state from deteriorating further? Theoretically. Are military leaders, generally, excellent judges of when such intervention would be in the public interest? Most of the history of military coups seems to indicate 'no.'