When I wrote my quick take on the affair, I hadn’t had the benefit of reading Peter Feaver. He writes:

President Obama may not want the painful confirmation hearings for McChrystal’s successor that a hasty departure would generate.And the McChrystal interview accurately notes that other members of the Obama AfPak team are already on beltway insiders’ short-lists to leave, opening up the possibility of widespread chaos at the top during the most critical year of the war so far. Obama might be wiser to bring McChrystal in for a tongue lashing and send him back into the fight as quickly as possible.
If Obama takes that course, he should also tongue-lash the other participants in this feud, namely his closest circle of White House advisors and his country team in Kabul. The Americans seem to be preoccupied with Washington enemies when they should be directing their fire at the real enemy — the one that is firing bullets, not insults, at them. Indeed, the dissension and back-biting that has characterized the Obama administration is precisely the sort of divide-and-conquer confusion we are trying to foster among the Taliban and Al Qaeda foes we are confronting in the AfPak theater. It is a tragic irony that we have proven more capable of sowing it among our own ranks than among the ranks of the enemy. . . .
President Obama has not yet achieved good civil-military relations in the conduct of his wars and he does not have much time to get it right.