Two books you oughtta read:
The Sacred Age of Terror (Benjamin and Simon)
Terror in the Mind of God (Jurgensmeyer)
They both address, to some degree or another, your last point re. preferring secular sons of bitches versus Islamist (Islam-ish?) theocracies. First one digs into the roots of radical Islam and its ultimate evolution into the modern AQ apparatus. Second one addresses the specific dangers posed by hard-line insurgencies with strong religious underpinnings. Heavy focus on Millenarian elements. Interesting, terrifying.
In regards to this article: I don't think anybody with little more than a network news view of Syrian events truly believes that this is a "good versus evil" situation. Yes, Assad is the quintessential "Very Bad Man." And, as it turns out, he's in a power struggle with a lot of fractious elements, some of which include other Very Bad Men. Who happen to be bankrolled by AQ, among other unsavory franchises. And this all happens to be playing out in the front yards of ordinary Syrian citizens- the only actors on the stage who aren't clearly bastards, and aren't really involved in the fight beyond fulfilling the role of propaganda/cannon fodder, and who probably won't benefit from any possible outcome. This is all pretty clear. But that's not the point of this article, is it? The point of this article is "are we really sure that those Sarin attacks were by Assad? Really?" The answer to which, at this point, seems to be a resounding "Yes." Followed by, "Please, Mr. Hersh, chill the fuck out with this shit." There are plenty of good reasons to bring all of the information to light that he did, chiefly to paint the Syrian situation with the shades of nuance that it deserves. The only bad reason I can think of to spit it all out at once is to try and fabricate doubt in a situation that doesn't merit it. Last August's chemical event points pretty clearly to Assad, for the reasons I brought up before. Are there other bad players on the board? Sure. But they didn't do this, not this time. So to point yet another finger at the Obama administration for acting on shoddy intel, or, worse yet, for inventing evidence and rationale for their own benefit? That's bad reporting.
Not to mention- talk about nuance- why would it be in the Obama admin's best interest to reach the conclusion that they did? It's not like Obama is chomping at the bit to overextend our military influence even further than it already is. Nor is it in his best interest to push an unpopular option (military strike) on a public still smarting from the WMD in Iraq "oopsie" and a congress basically creaming their jeans for the opportunity to put him in a moral/political/constitutional quandary. On top of that, and as we've both already established- it's not like the U.S. wants any of the current rebel opposition to Assad actually winning the war. That would be a fucking nightmare on so many levels. So what impetus could the administration possibly have for coloring the truth against Assad, as Hersh is arguing? You can call Obama many things, but catastrophically stupid is not one of them.