Option #2 is more likely. Back during the early Spring of '04, the Paki's went into Whaziristan villages (uncontrolled tribal area in Pakistan on the border with Afghanistan where we think #1 & #2 are hidding) and allegedly took out senior AQ types. They telegraphed their move days ahead and never showed any evidence of capturing/killing any prominent AQ types. Read show of force to pacify us after Powell's visit. Problem is we have no permission from Musharaf to conduct operations on his side of the fence.
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.