1st thing you have to think of is They are a Sovereign Country. If any other country sends its military into another they have a right to defend against this incursion.
2nd Politics - Pakistan is in a Hurt locker right now. They are fighting internal problems in the secured areas and in the country side they are fighting to keep the fanatics in their zone.
Parts of the military do what they want and pass Intel and support even when the central government does not want them to.
So is this a Political play so they save face? Is this a attempt to defend their sovereign borders? Is this an attempt to placate the extremist so they stick to agreements that have been made behind the scenes?
We do not know yet but time will tell.
Who know's they (Pakistan) may have agreed to the opns and this is just to make everyone believe they are mad.