Well, how about this...
Gather a massive force in the region, gather all the intelligence you can, and then make one massive sweep of the region, to grab up all the Taliban and Al Qaeda, including northern Pakistan. Then get the hell out.
I'm serious here. Frankly I think Pakistan has always been the largest problem in the region. I mean, they're the ones harboring the actual terrorists, the Taliban regrouped in Pakistan and then moved back into Afghanistan, and Pakistan is responsible for spreading Nuclear technology all across the region.
In other words, Pakistan is everything we said we were going to combat at the beginning of the War on Terror. Pakistan is what Iraq was supposed to be.
So if Pakistan doesn't want to cooperate with our offensive, tell them we'll ally ourselves with India and blow their country back to the stone age (a la Dick Cheney).
Once the massive sweep has been conducted, get the hell out. Then make it clear that if any major terroist attack occurs, we will find whatever country harbored the people responsible, and turn the capital of said country into a sheet of glass.