In his Special Comment Keith Olbermann argues that President Obama should not accept Gen. Stanley McChrystal's resignation. Steve Hynd at Newshoggers has this take.

McChrystal: Once A Petulant Jerk... (Updated):

And so the big question is: will McChrystal be fired for this? There's certainly enough reason to do so, but I don't think so, reading between the lines of SecDef Gates' statement (emphasis mine):

"I read with concern the profile piece on Gen. Stanley McChrystal in the upcoming edition of ‘Rolling Stone’ magazine. I believe that Gen. McChrystal made a significant mistake and exercised poor judgment in this case. We are fighting a war against al Qaeda and its extremist allies, who directly threaten the United States, Afghanistan, and our friends and allies around the world. Going forward, we must pursue this mission with a unity of purpose. Our troops and coalition partners are making extraordinary sacrifices on behalf of our security, and our singular focus must be on supporting them and succeeding in Afghanistan without such distractions. Gen. McChrystal has apologized to me and is similarly reaching out to others named in this article to apologize to them as well. I have recalled Gen. McChrystal to Washington to discuss this in person."

In my experience, that's the kind of statement managers issue when they're giving a petulant jerk a final, written, warning. It's not the kind they make when they're looking to fire someone. It's full of language suggesting the miscreant realises his mistake, is sorry, and won't let it happen again. What it doesn't contain is anything suggesting the miscreant has crossed a line. So, I expect that McChrystal will get some kind of reprimand on his record, but won't get canned. Bringing political strategy into it, as it must, that's probably how the White House is thinking too. If McChrystal gets fired for insubordination, even despite his previous record of speaking - and leaking - out, then the G.O.P. and Democrat hawks will always say that the mission in Afghanistan suffered because of it and will make political hay from that conjecture. From the White House's point of view, better to wait another six months, perhaps, and fire McChrystal for actually failing.

I agree this is a lose/lose for the President no matter how he handles it. I don't agree with Keith that we're going to see a "humbled" Gen. McChrystal that will help him redefine the mission in Afghanistan. We need to redefine the mission there, but I don't see how McChrystal is the man to do that and tragically Obama does not appear to have any interest in getting us out of there either.

Personally I think he should accept his resignation, but given the political climate as Keith and Steve pointed out, I would suspect they're right and he keeps him, at least for a while.