Let's be blunt: Pakistan has to eliminate every last vestige of Al Qaeda from its territory. Pakistani complaints of sovereignty violations after May 2nd met no echo in the U.N. or elsewhere. That's because under the post-9/11 U.N. Security Council resolutions (especially 1373) Pakistan has the binding sovereign obligation to eliminate terrorists, terror havens, and terror-training camps from its territory. Willful blindness or compliance with terrorists = no claims to sovereignty.
So as long as Al Qaeda has a refuge in Pakistan it's an invitation for others to invade Pakistan to get at them.
