The disagreement on Pakistan's stance has as much to do with leverage as it does with right or wrong. Negotiations take place on a playing field leveled based on the underlying leverage of each party; thanks to your real world experience, I'm sure you'd understand this better than me.
The problem is the position of the USA is one of want, not need. The Americans, as the premier superpower have endless routes to choose from and can strong arm a whole host of nations to let them funnel in supplies. They insist on using the Pakistani route, because it is cheaper, not because it is the only route. There in lies the problem, the Americans can easily switch routes at a cost that will be irrelevant in what has now become a trillion dollar adventure over the last decade.
The fact that they haven't speaks to their confidence that they hold enough of the cards to pressure Pakistan into eventually giving in; were this to not take place, they can just as easily use that to their advantage. By constantly refusing to let supplies through, Pakistan is playing into the perception of a nation that is unwilling to help, and at worst, standing in the way of the fight against extremism and terrorism. While you and me agree that is largely unfair and incredibly biased; as the foremost military and media power, the American opinion and spin carries far more weight. By using Pakistan's position to incriminate itself, the US is doing far more damage to the Pakistani position from a political as well as an economic standpoint.
While we may disagree on the correct way to go about this, I fear the worst case scenario for Pakistan in this negotiation is far worse than the one faced by the Americans. If we lose this time, we may have just sacrificed the long term prosperity and strategic relevance of our nation. If the Americans come out on the bottom, they will simply swallow the loss of a few extra billion and find another way...or my greatest worry, become far more aggressive in enforcing their will on Pakistan. The unfortunately reality is that no one has the ability to withstand the true force of American aggression, the paranoia of which was enough to destroy the USSR.