IMO it's going to be tough if we don't have the gov't backing. Up until now there's been tacit agreement with some of the more moderate elements of their leadership to do limited, targeted, engagements with specifically-approved military objectives (following a person of interest across the border to a cave in Kashmir, for instance). So it's been either missile attacks or special-forces stuff...guys who are trained to do the hairy stuff.
From everything I've heard, much of the army occupation of Iraq force will be transferring to Afghanistan (and Pakistan if it flares up). Northwestern Pakistan is barely (if you can call it that) controlled by the central government. If there's any public outcry to "keep the Americans out", you can expect guys with pitchforks and shepherd's crooks fighting next to the guys with Kalashnikovs against us. If they go to martial law for some reason, or the military just goes under the control of the bad guys and takes possession of their nuclear capability, then it's bad juju. You have our soldiers who've been trained for the last few years for house-to-house urban fighting and patrolling, in a new environment, even more spread out forces in unfamiliar and rough terrain, with the uncertainty of nukes (a possibility we always have trained for, but would make me apprehensive).
Bottom line, though? If we can do unlimited air strikes and UAV reconnaissance, it gets a lot easier to meet the objectives. We'll have almost overwhelming force levels for what we'll be trying to do (a lot of the same stakeout-and-takeout of the Bad Guy Upper Echelon we did in Iraq), that could only possibly be affected if they go nuclear. At that point, I can't even speculate....except it'll be much worse for them than us.