One of the few new nuggets of reportage in Jonathan Alter's
was the story of the confrontation between Obama and the Pentagon, in which McChrystal played a major role. Alter bills the conflict as nothing less than the most important civil-military issue since MacArthur v. Truman, and I think that's about right. Part of the issue was that McChrystal was using the media to undermine Obama and limit his options. Obama handled this well and then (I assume) leaked the story to Alter in order to cement the agreement the White House reached with the DoD. By any stretch, the McChrystal story is a major violation not only of routine protocol between the commander-in-chief and theater commanders but of specific pledges. And that is insubordination, a firing offense.
That is not to say that Obama will not suffer regardless. But in the long term he will have to make the right call.
Postscript: Maybe sooner.