I just read the Rolling Stone piece and found the tone of disrespect somewhat stunning. The media immediately references my piece on Fox Fallon from 2008, but I'm more impressed with the differences than similarities-- as in, Fallon disagreed with the president on substance while McChrystal's gripes strike me as stylistic (e.g., Obama struck him as uncomfortable before brass) and superficial.
Fallon never said anything disrespectful of his superiors in front of me, nor did his staff. The admiral just fundamentally disagreed on the possibility of going to war with Iran and wasn't shy about sharing that opinion in the press, which he did repeatedly prior to my piece (which he later said misrepresented his views while quoting him accurately--to the tune of over 1,500 words).
Here, McChrystal does just the opposite: never really disagreeing with his superiors while openly disrespecting them. I say "openly" because he and his staff did it repeatedly in front of a reporter they knew was there to report on what he saw and heard--just like I did.
Is that enough to get him fired? That's Obama's call. The fact that McChrystal is quoted both directly and in a secondary manner (through his staff) making truly derogatory remarks about so many principals (VP, NS adviser, our AMB in-country, Holbrooke) is problematic going forward, but firing the right guy for the right job when he agrees with your policy is likewise a hard choice for the president.
In the end, it all comes down to the relationship itself. A magazine story can damage such a relationship but it cannot define it. Fallon was on thin ice with the White House when my story appeared, making it the final nail in the coffin. If Obama's relationship with McChrystal is solid, the Rolling Stone story won't be enough to trigger his sacking. But if it was already fragile/strained, then it may become the excuse. But my guess is that McChrystal and Obama-Biden are on an entirely different trajectory over Af-Pak than Fallon and Bush-Cheney were over Iran.