In an effort to express their gratitude for the new Pakistani government's so-far implicit condoning of their operations, Al Qaeda recently bombed a Marriott hotel in Islamabad where the Pakistani president was supposed to be hosting (but had changed venues at the last minute).
The attack was either an effort to take out the Pakistani leadership and try to crumble the government, or to simply send a message--we liked our deal where you left us alone. Now Americans are coming and shooting us. If you don't stop this, we'll keep bombing you.
The Pakistanis are in deep debate. Nobody's questioning that they should keep Americans out of Pakistan. But with these bombings and implicit demands for it, pushing back at the Americans will look like pretty bold appeasement. Doing nothing will bring more attacks. The Pakistani executive has to stand up to the Americans in some way, or else he will look weak. Pakistan is in a difficult political position.
But most of Pakistan's troops are still outside of its Northwest Frontier regions, and only Allah knows why. With bombing attacks within Pakistan increasing by the week, the greatest crisis the Pakistanis face is whether or not they can get control of their own territory--territory that they have claims of sovereignty over. But sovereignty becomes weak when a government does not police or administer a territory at all (such measures are used when claiming islands or other disputed areas); Pakistan may complain, but their international lawyers should be warning them that they need to get troops into the northwest, lest a lame-duck president try to settle the score with Al Qaeda once and for all.