Today’s O’Hanlon piece (web briefing) might be the best thing yet written about the fight over his comments:

Certainly, if given a do-over, McChrystal might make different, more nuanced statements; he was indeed too blunt and impolitic. But the criticism goes too far.
The Obama/McChrystal plan is classic counterinsurgency and focuses on protecting the Afghan population while strengthening Afghan security forces and government. McChrystal was asked about a “counterterrorism” strategy that would purportedly contain al-Qaeda with much lower numbers of American troops, casualties and other costs. McChrystal did not try to force the president’s hand on whether to increase the foreign troop presence in Afghanistan. The general critiqued an option that is at direct odds with Obama’s policy and conflicts with the experiences of the U.S. military this decade. That is not fundamentally out of line for a commander.
The past eight years have proven that a counterterrorism option for Afghanistan won’t hold the country together. This approach, the essence of the Rumsfeld “light footprint” concept that dominated most of the Bush presidency, led us to place most American troops in Afghanistan under a separate command from NATO because the Bush administration generally eschewed NATO’s peacekeeping mission. The counterterrorism operation was seen as the critical ongoing role for U.S. forces after the Taliban fell, but by last year its fruits were clear: a resurgent Taliban movement operating effectively in 140 of Afghanistan’s 368 districts; a tenfold increase in the rate of NATO casualties; an al-Qaeda leadership in western Pakistan swearing allegiance to the Afghan Taliban and probably hoping to reestablish a sanctuary in Afghanistan….
Perhaps it is acceptable that we consider again abandoning Afghanistan to the Taliban and related movements, and trying to limit al-Qaeda’s future role there with long-range airstrikes or the occasional commando raid. But if so, let’s not pretend that Afghanistan will remain intact. The essence of McChrystal’s comment last week was that if we scale back dramatically as envisioned by the counterterrorism approach, Afghanistan would become “Chaos-istan” again. That comment is almost unassailable as far as it goes.
And McChrystal understated his case. The counterterrorism option would probably also fail to kill and capture terrorists; even its immediate goals are likely to be unattainable. As my colleague Bruce Riedel and I, among others, have argued, a counterterrorism option would lead to a loss of crucial human intelligence networks; once NATO forces drew down, the Kabul government would probably fall, and the resurgent insurgents would take revenge on those previously associated with us. Air bases from which we fly unmanned vehicles today over western Pakistan would also be lost, meaning that remote strikes would have to come from ships several hundred miles away. Pakistan’s interest in restraining the Afghan Taliban would probably diminish, as it would rather see that group back in power than an India-friendly regime in Kabul.