Given the reality that no two allies - in this case the US and Pakistan, can ever have total unanimity of their positions on international issues and can never barter away their core national interests it should never be expected that Islamabad and Washington would have totality of concord as they now grapple with the hoped/feared consequences of foreign involvement in the Afghanistan imbroglio. They need to agree to disagree and moved forward on what they share and if possible expand on that.
Given the wide spectrum of economic and financial Pak-US bilateralism there is not much to tinker with; it has its own dynamics and strength to withstand minor and moderate shocks if and when they come. Why the two sides haven't been able to evolve common approach on drone attacks, that's a question. Certainly the two sides don't differ on the need to take out terrorists, but it is the one-sidedness of the drone operation that does not sit well with Pakistan. Should the two sides share intelligence and improve tactical co-operation it will not only spare wonton loss of innocent life but also fit in the definition of a joint operation.