First, let me say this: I believe General McChrystal is not the smartest man in the room, he's the smartest man in the county.
Second, I believe that every man has limits, especially when fighting a war, and trying to prosecute an incredibly difficult and detailed strategy without support from above.
Third, the rolling stone article does attribute some things that no General (or Officer, for that matter) has any business saying, in a public format, about the commander in chief, or the vice President (regardless of how true those statements may be.) I see this as the actions of an extremely frustrated leader, who is trying to do something that his superiors simply don't understand, and based on their apparent priority for listening to him, don't care to learn.
However, General McChrystal chose to resent himself and his staff to the writer from Rolling Stone. I doubt he did this without forethought. I believe that he knew exactly what he was doing, and rather than retire and then join the ranks of other rock-throwing has-beens, he chose to make a bold statement, one which would get a lot more press coming from the current commander in Afghanistan. He would illustrate the issues with the chain of command in a manner that would end badly for him, but would get the maximum amount of coverage possible. It is an act of a leader desperate for people to understand that the greatest enemy we could face in Afghanistan is mismanagement and lack of support from our own government. It is an act that can only end badly, like jumping on a grenade--there's a slight chance it won't detonate, but the odds are stacked very high against you.
General McChrystal should now do the second hardest thing he's ever considered: He should walk into the White House and resign, stating clearly, in writing, his reasons, including the issues with his ambassador, the commander-in-chief and vice president. This is a fight he can not win, and retain his rank, so he will sacrifice his stars on the altar of freedom. He shouldn't even give the CiC the opportunity to yell at him, just put the resignation on his desk, salute, and walk out of the office. He should send copies to every news organization he's ever dealt with, and then talk to the press pool. Let his message get out, let his story be told, and then he can start campaigning for 2012.
People at this level play for keeps. In an administration which has been described as extremely sensitive to criticism, I see no way for General McChrystal to stay in position, regardless of any apology he may issue publicly. They may offer him the chance to publicly apologize, claim that he is under severe stress and was taken out of context, then allow him to quietly retire in six months, but I doubt that will happen. No matter how critical he may be to the war, this administration (and any administration, I suppose) will not tolerate those in Uniform challenging their ability to lead. As American Soldiers, we are beholden only to the Constitution, but we answer to the President.
Finally, I really think the the General chose to fall on his sword for a reason, not just because he felt like shooting his mouth off to a Rolling Stone journalist. I believe he wanted to make a very clear statement about the mismanagement and outright lack of understanding of the war we are fighting and the strategy we are using at the very highest levels of government. I believe he chose to make this statement at this time, because the afterglow of Hope and Change is finally fading and his words will ring true with many. I believe he chose to sacrifice his job, his career, and to risk his future livelihood so that people would be made aware of the challenges faced by the troops fighting the war--that they face an enemy in Afghanistan with lines of indirect support running all the way back to D.C.
At least, that's one explanation.
Another member of the Vast Anti-Yon Conspiracy weighs in on Yon and President Obama and their agreement of the facts.
P.S. Mike Yon is doing cheetah flips now, exclaiming that he was right, that McChrystal is unbalanced, just like he said months ago, that his staff was on drugs (alcohol) when they shit-canned his embed, yadda yadda yadda. I believe I've outlined but a few reasons that directly point to General McChrystal's clarity of thought and reason. And no Mike, You can't go from "I was disembeded because they are all crazy monkeys" to "I was disembedded because there wasn't enough room to keep me, not because I am a loose cannon who will violate OPSEC for another $0.10 in paypal donations" to "I was disembedded because there wasn't enough room to keep me, that's what this letter from the PAO , Admiral Smith says," to "I was disembedded because there wasn't enough room to keep me, at least that was their reason, not the real reason" to "You are all clowns! This is a vast conspiracy! You are plant from Blackfive, not a real supporter!" and "You disagree with me, you are a member of the cabal of evil Blackfive supporters who are all against me! You are banned!" and still expect people to believe anything you say about this. Asshat.