Does a policy of military strikes within Pakistan carry any significant repercussions in the short term?

Pakistan has screamed national sovereignty since the beginning of the GWoT. We allow them this, this allows them to scream foul anytime the US Military encroaches on their borders but they don't stop us, We warn them in advance and they inform us of targets within their borders they cant get to but suspect to be Al-Qaida. It allows them to save face in the eyes of their countrymen and the Muslim community as a whole.