i think she's missing it. the idea is that all that hegemony stuff is more effective if people are willing participants. i know i'm putting some words in there, but it's really the whole point; this sort of "peace research" is not about reversing the hegemony, it's about institutionalizing it.
so, are the actors using ideas about history and religion and other things to create chaos in the region? yes. to an extent. i think the american military has demonstrated it's ignorance about things a few times. for the most part, though, i think these things are intentional or at least made intentional when they're pointed out; the bush administration may not have foreseen the sectarian fallout, but the military presence in the region has sure done everything it can to use it as a divide and conquer technique. so, it seems naive to suggest that they don't know any better when they're clearly going out of their way to cause all kinds of mayhem.
but i think that's missing the actual point that he's making - what they don't realize is how much more successfully integrated these regions would be if less violent tactics were used to subdue them. and, to a major extent i think he's basically right. there has to be significant wealth redistribution in this region.