Earlier quoted context omitted.
Last I looked the US weren't at war with Pakistan.
But the U.S. is at war with ISIL, as part of a joint task force involving the Pakistan armed forces. It's not total war, so the real issue is whether or not the CIA drone assassinations killed innocent civilians. The article mentions how drone attacks have killed civilians, but it doesn't specify if those are the CIA requested attacks or if they were approved by Clinton.
ISIL and Al Qaeda are more enemies than friends at this point in their histories.