I really don't understand why we allied with them in the first place; I know they have nukes and are an easy access point to get to Afghanistan, but couldn't we just rely on India and a few of the Central Asian 'Stans?
Diplomacy and such do not operate in a vacuum. Historically speaking; the 50+years before 9/11, the US had much better foreign relations and military ties with Pakistan than with India. There were strong links in the military and intelligence communities. Shortly after our post Cold War distancing from the immediate region these ties weakened and in many ways the two countries have been following different aims and objectives since. However, for present/future intelligence and logistics in the conduct of the war on terrorist organizations it is absolutely vital that we try to maintain strong links and friendly relations. Granted this is often distasteful and unpleasant for both nations. The tribal regions of PK are still a hot bed of international terrorism, and these can easily be exported further afield, as witnessed in Mumbai attacks and plots in UK and US. The problem is best solved and the wound best stanched locally. As much of Bush foreign policy demonstrated, it is fool hardy and dangerous to just dismiss potential partners and take unilateral action regardless of consequences.
