It is hard to believe that President Obama and his staff will be able to continue to work with McChrystal after the revelation of the Rolling Stone affair. President Obama will have to defend his commander-in-chief powers under Article II of the Constitution and that will almost certainly require McChrystal's swift retirement. To allow McChrystal to apologize and stay on would set a bad precedent, send the wrong signal regarding civil-military relations to the rest of the military, and would cause great uproar among Obama's civilian staff.
Who will replace McChrystal? For the sake of continuity in the midst of the critical Kandahar operation, the elevation of LTG David Rodriguez would seem logical. Regrettably, the contemptuous attitude toward Obama and the White House staff apparently extends throughout McChrystal's staff. As a McChrystal deputy, Rodriguez may be suspect. In any case, several staff officers will also have to go, with a broad investigation likely to follow. Thus someone from the outside may be necessary. Probably not Gen. James Mattis -- Defense Secretary Robert Gates apparently passed him over for Commandant of the Marine Corps so Gates could hardly support him for ISAF. My guess would be someone currently working on the Joint Staff or on Gates's personal staff, someone already well known to Gates and Admiral Michael Mullen (which, ironically, is how McChrystal and Rodriguez got to Afghanistan).
Finally, how did this fiasco with Rolling Stone magazine happen? Field commanders and their staff officers talk to the media in order to get their stories out. In the case of McChrystal and the Afghanistan campaign, the need to do so has lately been even more urgent than usual. McChrystal and his staff were seeking to "add time to the Washington clock." They hoped to get their message out to media audience segments that would soon be putting the most pressure on the Obama administration to terminate the campaign. The theory was that delivering their message -- through a channel like Rolling Stone -- would short-circuit, at least for a time, growing political pressure against the war. Unfortunately for McChrystal and certain members of his staff, the inflammatory bits of the article apparently show a commander and staff frustrated and exhausted by an intractable task -- the very opposite of the message they intended to send.
Obama, Gates, Mullen, and Gen. David Petraeus will get an opportunity to make a decisive shake-up. But counterinsurgency is all about inspiring confidence in the cause among the many actors inside the host nation, not to mention the soldiers and Marines who are ordered out on patrol every day. What remains of that confidence after the shake-up remains to be seen.