Not only is it immaterial whether Petraeus's graduate thesis is a bit hollow, to argue over it takes you down the wrong path. This whole dispute over whether Petraeus is a genuine saint or a false messiah is part of the same conversation, the one that goes "is David Petraeus man enough to fix everything that has gone wrong in Iraq?"
But that's a bad conversation. It buys the premise that individual American leaders can still fix Iraq so long as they have enough wisdom and pony bait. But whether Petraeus actually shoots insurgent-killing lasers from his eyes or not, Iraq's problems are too substantial and deep-seated to be fixed by an outside country, much less a mere individual. The argument, as relates to Petraeus, isn't whether this man is good or bad. It's whether this situation remains at all susceptible to our military's efforts, or it's now a matter entirely dependent on factions internal to Iraq. If you want to argue against Petraeus, the argument should really be that he's beside the point.