Peter Bergen writing in The New Republic in defense of an ambitious approach in Afghanistan says the Taliban and al-Qaeda have largely merged so there’s no sense in thinking we can fight al-Qaeda without also engaging with Afghanistan’s civil war. To my mind, Bergen’s account of the situation largely begged the question—he says we’re fighting the Taliban because the Taliban is working so closely with al-Qaeda, but arguably the Taliban is working closely with al-Qaeda largely because we’re fighting them.
In general in these foreign occupation scenarios it’s difficult to disentangle cause and effect. If 70,000 Taliban fighters showed up in the United States for any purpose whatsoever, I take it that Americans would all band together to fight them off. But our unity of purpose and anti-Taliban resolve in the face of foreign invasion wouldn’t tell you very much about our post-invasion behavior. Meanwhile, according to Marc Sageman (PDF) al-Qaeda Central in Pakistan doesn’t even have very much to do with the majority AQ-branded terrorist attacks.
Realistically, I think you’re looking at uncertainty one way or the other.