There is clearly an important difference between the behavior of intelligent and stupid people(ie, Obama vs. Sarah Palin, Hillary Clinton vs. Michelle Bachmann, etc.)
Having said this, it is clear that Gen. McChrystal is intelligent, not stupid. Occam's razor says the simplest explanation for any complicated problem is probably the correct one. Therefore, the simplest explanation for McChrystal's behavior is below the fold.
Gen. McChrystal finds himself in a difficult position. The president has supported his strategy in Afghanistan, including supplying a large increase in troops. However, McChrystal's strategy seems not to be working. Marjah has not gone the way he planned, and Kandahar is looming, as a much greater challenge.
Therefore, I suspect that his allowing his staff's astonishingly unguarded comments in the presence of a Rolling Stone reporter, with the equally astonishing lack of any ground rules, was deliberate. I suspect he was hoping that he would be dismissed, and, like W., be able to leave the mess he made for someone else to clean up. In fact, he was very much a Bush supporter, and admirer, unlike most other people with an equal intelligence.
Given this, I believe the best way to handle him is to keep him in a responsible position in regards to his own mess, but to appoint a handler, to put someone like Gen. Rodriguez in a position close to him, where McChrystal would have some responsibility, but would have a close-up checker.