This mind-boggling article in Rolling Stone is the hot topic of the day, for good reason. If it's accurate (it's a bit gossipy, so I regard it as accurate but not quite the full picture) then McChyrstal and his command really have lost their minds. One of the reasons America has lasted so long as a democracy is that the military has never developed the mentality that it is a source of authority separate from the elected government. This is not to say that individual generals haven't stuck their noses into the political arena at various times, just that it hasn't been done by the military as a whole. In order to remind the military of it's place, McChrystal needs to be beaten down. Hard.
It's one thing for the military to question the goals of an assignment given to it by the civilian government, though that needs to be done through the hierarchy. But it's entirely different when a military officer mocks elected officials and others civilians. It's simply not acceptable. Individual officers serve at the whim of the president, though that official should (and does) usually defer to the military's promotion system. The top generals are different, however, and Obama should not hesitate to remove McChrystal from responsibility for an ongoing conflict.