First, let me say this: I believe General McChrystal is the smartest Army General in the country, only one or two Marines are smarter.

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.) The UCMJ (Uniform Code of Military Justice) and the unwritten rules for Soldiers in the US Forces are crystal clear in this point.
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, he chose to make a clear 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 had done the second hardest thing he’s ever considered: He walked into the White House and resigned. This is a fight he can not win, and retain his rank, so he sacrificed his stars on the altar of freedom.
People at this level play for keeps. In an administration which has been described as extremely sensitive to criticism, I saw no way for General McChrystal to stay in position.
No matter how critical he may be to the war, this administration (and any administration) could 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 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 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.