The US government funds much of the Pakistani military and intelligence agencies. Around $18 Billion dollars in the last decade of official aid, of which more than half is military - not sure if there are even figures for the last few years but they've presumably grown. That's a lot of incentive in some very powerful parts of the government to allow the US carte blanche to kill whoever they want to. One day some of that money will probably be used for an attack on US soil.

https://en.wikipedia.org/wiki/Foreign_aid_to_Pakistan#U.S._f...