Go read this first:
Now, let me just say that I am greatly simplifying things for the purposes of this post. This is no treatise on American-Pakistani relations; I don't have time to write that right now, but I wanted to express my frustration and dismay over the situation. Furthermore, let me add that I am a social & fiscal moderate and a conservative on most foreign-policy issues (save the Iraq mess). We have room for diplomacy when bullets aren't flying, but when someone is abetting your enemy, will not act on their own to expel the enemy, and threatens to attack you for prosecuting your campaign, eventually diplomacy is no longer viable, and action must be taken.
I understand that Pakistan is yet another of these lame Old World countries so riven by ethnic differences that it doesn't want to be Pakistan. And if you plan to counter that it's a symptom of colonialism, I maintain that the phenomenon is not limited just to former colonies (e.g. Belgium). The difficulty in maintaining central power over people who care nothing for Pakistan is that you are powerless to respond to your "allies'" security concerns without starting a civil war.
Pakistan's recent assertion that it will fire on American troops in its country surely seems justified in their eyes, but Osama bin Laden or at least the Taliban leadership IS in Waziristan. There's little doubt about that, and they are our true enemies. Pakistan is simply the current hiding place of the Taliban and Al Qaeda, much like Afghanistan was until we swatted them. The differences between Pakistan and Afghanistan, aside from the superficial, are important. One, Pakistan has fought several wars with India over the disputed Kashmir region and various other post-colonial pissing contest nonsense. This wouldn't be that big a deal, but India's strategic (as a front against Chinese expansion/aggresion in South Asia) and economic importance to the world means that we have to act thinking about how our actions impact India (which impacts us). Two, if we piss off Pakistan, they have nuclear weapons. If a crisis with India were to come to a head, who could know which of the two might use the nukes on the other? It's not worth the risk. A third somewhat unrelated issue with Pakistan is the potential wave of negativity that could erupt from a flawed sense of Nationalism (even though the radicals don't want to be part of Pakistan, unless it's a religious state), breeding even more people who hate the United States enough to attack it and its interests.
So, given that the Taliban and Al Qaeda can still cause havok from Pakistan without fear of counter-attack, what can we do? Pakistan says that they will shoot back. They don't really want a war with us. I say that if Pakistan is harboring Taliban (harboring, even by omission/inaction), and they want to risk it, let them shoot at us and see what happens. We cannot continue fighting a war in Afghanistan with one hand tied behind our backs. If Pakistan fires at us, strip them of all the federal aid that they receive and essentially spend to arm themselves against their own populace.
An ally doesn't give aid, abettal, succor, arms, and tacit approval to your enemy. Pakistan needs to choose sides, and suffer the consequences of whichever one they choose. They've been playing both for far too long. If they don't want to help us, fine, but if they shoot at us, I say stand back. We will never end this war unless we are decisive now. The enemy is the Taliban. The Taliban is in Pakistan, openly. If Pakistan's government doesn't help, they too are the enemy.