It is also a way for him to agree with the local mideast version of events which always depicts US attacks as atrocities committed against innocent wedding parties and back yard barbeques. Al Qaeda members routinely pass in and out of Karachi under the protection of various allies while Musharaf looks the other way. They have heavily fortified compounds within the city. The US doesn't want to run the risk of causing a revolution in Pakistan and letting some nut job get his hands on their nukes. We give him f16's in exchange for information and he takes a neutral stance against the percieved western agression. Similar to our understanding with the Saudi Royal family.
Exactly my point, friend. We have to carefully pick and choose which targets to pursue in Pakistan at the risk of causing the Musharaf government from being overthrowm by anti US elements accusing Musharaf of being a servant of the Americans. As you correctly stated, we do not want this to happen and have a bunch of pro-AQ/Taliban nuts take over the Paki nukes. Hence, if we went over, the reasons must have been good. Like it or not, we must deal with the sensitive political situation in Pakistan while hunting the vermin hidding in the region.