In the aftermath of the (apparently) failed attempt to kill Al Qaida's #2 man, Ayman al-Zawahiri, there's a lot of hand-wringing and official indignation going on. Collectively, this is little more than an effort to cover the tracks of a joint operation that missed its intended target.
I say "joint" because it's virtually impossible that Pakistan had no prior knowledge of the planned strike. American surveillance drones had been criss-crossing the border area for days, in an effort to pin-point Zawahiri's whereabouts. Islamabad was also aware of a U.S. attack in early December that killed Al-Qaida's #3 leader; that strike was remarkably similar to the attempt on Zawahiri. In both cases, the attacks were carried out by Predator drones, ostensibly operated by the CIA. The strikes came after intensive intelligence efforts to locate the designated target. When the December attack succeeded, Pakistan quickly offered a cover story, saying that the Al Qaida figure died in an "accidental" explosion.
Unfortunately, the recent attempt on Zawahiri inflicted collateral damage that was quicked publicized by the western press and Arabic media, leaving Islamabad in a difficult position. The Pakistani government quickly moved to distance itself from the strike, summoning the U.S. ambassador for the obligatory protest. The Musharaff government also made vague statements about "preventing similar incidents from happening again."
Such rhetoric and posturing is strictly for public consumption. Behind the scenes, the Pakistanis will continue to cooperate with the U.S., since the Al-Qaida presence in the tribal regions poses a direct threat to regional security and the governmenit in Islamabad. Diplomatic notes and political protestations aside, the Paksitanis really have no other choice.
One final note: while the hunt for senior Al-Qaida figures never stops, the hunt for Zawahiri intensified dramatically just before the recent strike. For at least a 24-hour period during the week of 7 January, Predator video feeds from Afghanistan were cut off to outside agencies, to prevent a possible tip-off of the search target--and the pending strike. Such a move is very rare, and it shows the level of effort associated to the surveillance mission and resulting attack. However, UAV imagery is rarely enough to justify a strike. Heightened Predator surveillance was likely an attempt to confirm other intel reports. Given the successful strike in December--and the effort to "get" Zawahiri a few days ago--it seems evident that the U.S. has better intelligence on the whereabouts and habits of senior Al Qaida leaders; possibly from within the group itself.