With McChrystal out and Petraeus in, much of the hand-wringing presented by Matt here is moot. The comment section, as usual, is full of concern-trolls, left and right, both blaming the Obama Administration for the entire affair. It seems that having an internal policy debate is wrong! This never happens during wars!
First of all, McChrystal (and by extension, the military establishment responsible for the tactical operations and strategic goals in Afghanistan) are not about "total victory" a la Doug MacArthur in Korea. The latter historical analogy is important to keep in mind, if only because the lesson from Korea was that MacArthur's insistence on "victory" not only cost him his job; it brought the Chinese in on the side of the North Koreans, clouded the judgment of Truman's inner circle (especially after Inchon and the collapse of the North Korean offensive), and was contradicted by the terms of the UN Resolution authorizing force on the Korean peninsula, which was always and only to push the North Koreans back across the 39th parallel.
In this case, McChrystal has always maintained the the military is an adjunct of a broader political settlement in Afghanistan, undermined by the increasingly obvious corruption and authoritarianism of the Karzai regime. The upcoming offensive, talked about for months, is supposed to end any Taliban hopes of a resurgence, and if the Pakistanis cooperate, might actually succeed (their own offensive against the Taliban in their northwest seems to have turned a real corner, particularly in the Swat Valley). With the plans in place, and logistic and deployment questions in all likelihood cemented months ago, McChrystal is not necessary if the United States military is as professional as it claims. Since Generals at this level are more administrators than fighters, any competent general should be able to get this ball rolling and keep it rolling.
Of course, the political question of the confidence of the troops might be important if it weren't for the fact that McChrystal doesn't seem to be able to muzzle his staff. He got the firing he deserved, as far as I'm concerned, and while Petraeus isn't exactly my pick - Lieberman likes him too much for my tastes - he does have the experience and basic competence to carry out the upcoming military operations without embarrassing himself.
Whether or not there is or should be a debate over our presence in Afghanistan seems to me to be on a par with having a debate about global warming because there is an on-going leak of oil on the floor of the Gulf of Mexico. The two are related, to be sure, but dealing with the immediate issue and the long-term, overarching strategic issues are and should remain separate.