At a time when violence in Afghanistan is sharply rising and several central planks of the president’s strategy to “disrupt, dismantle and defeat” the Taliban and Al Qaeda have stalled, many of the president’s top advisers have continued to criticize one another to reporters and international allies alike, usually in private conversations, and almost always off the record.

“Yes, we do hear them disparage each other,” said a senior European diplomat who works closely with the United States on Afghanistan strategy. “It’s never good to hear that.”

Bruce O. Riedel, a senior fellow at Brookings Institution who helped the administration formulate its initial Afghan policy, added, “This flap shows once again that his team is not pulling together, but is engaging in backbiting.”

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All of [his aides] remain loyal — fiercely loyal — to McChrystal and to his counterinsurgency approach to warfighting. But they feel like McChrystal was done in by his inner circle, by an adversarial reporter, and possibly by the strains of seven years of near-constant war. Few recognized the man portrayed in the Rolling Stone piece. Several expected President Obama to let McChrystal go tomorrow.

“It’s heartbreaking for me,” said one International Security Assistance Force officer who worked in Kabul. “He’s the best officer we have over there. Rolling Stone’s portrayal of COIN [counterinsurgency] and of McChrystal’s strategy as some fringe approach is silly. We’re fighting the best strategy we could possibly fight. It’s still not a great strategy, because the time for a great strategy passed six years ago. We missed whatever golden opportunities we had by taking our eyes off the ball in Afghanistan when the insurgency barely existed. Now we’re doing nation-building under fire. The effort can still be salvaged, but McChrystal was the best man to salvage it.”

***
Nonetheless, and this is the damning third point, the fact that it’s “just staff officers” talking like this doesn’t let McChrystal off the hook. In fact, the story suggests that, on some level (and how serious a level is something for Obama and Secretary of Defense Robert Gates to find out), McChrystal’s operation is out of control.

McChrystal is clearly a charismatic commander: ascetic, tough as nails, strategically smart, and as demanding of himself as he is of those around him. These sorts of commanders inspire deep loyalty from their inner circle, especially in wartime. In McChrystal’s case, it has inspired idolatry. It’s been widely observed that his aides see themselves not merely as aides but as disciples to a warrior-god…

What seems clear is that McChrystal has sown, or in any case tolerates, an atmosphere of disrespect for the civilian chain of command. And the fact that his entourage feels free to talk like this in front of not just him but a reporter—much less a reporter from Rolling Stone—speaks volumes about how far they’ve burrowed into their cocoon.

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“It’s just really bad—really, really bad,” media mogul Saad Mohseni, the head of Afghanistan’s biggest broadcast outlet, Moby Group, told me from Kabul. “I think it will be an extraordinary loss of opportunity for Afghanistan. He is very close to President Karzai, which no one else in Washington is. To see McChrystal go is to lose ground and have to restart the whole effort from scratch. He is very determined to get the job done, so it would be a big loss for the country.”

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Even if he remains the U.S. commander in Afghanistan, McChrystal is almost certain to emerge from the furor as a damaged figure, less able to defend his war strategy against those in the administration hoping to change it.

“I strongly believe McChrystal will return, but the damage is done,” said a senior military official sympathetic to McChrystal.

Among the issues Obama will have to decide is whether McChrystal can remain effective as commander in the wake of the furor. “Does he come back weakened or gun shy or hesitant to make that case?” asked one senior official. “We need him engaged.”

***
Gen. Stanley McChrystal is a hero—a selfless, fearless and inspiring soldier. He is also something of a military genius. In Iraq, as commander of the Joint Special Operations Command from 2003-2008, he created an extraordinary military operation.

His command center—a vast open hall resembling the floor of a trading exchange—put long-haired civilian geeks next to wiry commandos, and together they uncovered, analyzed, pooled and acted on information that enabled soldiers to launch successful operations at a moment’s notice. They did so in ways that only a few years ago would have required weeks of preparation and rehearsal. He is one of the fathers of victory in Iraq, because his organization dismantled the leadership of al Qaeda there. Few Americans know, or will know, how well he has served this country—and as a shrewd, humane commander, not merely a lethal one.

President Obama should, nonetheless, fire him.