This LAT piece suggests that the US drone campaign in Pakistan really has been quite effective:
The stepped-up Predator campaign has killed at least nine senior Al Qaeda leaders and dozens of lower-ranking operatives, in what U.S. officials described as the most serious disruption of the terrorist network since 2001.
CIA officials had suspected that their targets were being tipped by Pakistani intelligence to pending U.S. strikes; bypassing the government ended that concern.
It also eliminated delays. Former CIA officials said getting permission from Pakistani authorities could take a day or more, sometimes causing the agency to lose track of the target. The missed opportunities were costly because it often took months to assemble the intelligence necessary for a strike.
Seems like the right decision.