They are using the same perverted logic provided to them when they were fighting the muslim govt. in Afghanistan and muslim afghan army as well as the muslim majority state govt. in Kashmir and muslim majority police force there.
(1) GoP is a puppet govt. under the control of the US and so is the PA/ISI. They not only provide supplies and support to the "crusaders" but actively fight and kill "good" muslims like in Lal Masjid themselves if they ask for establishing "sharia" in state.
(2) Because of these actions GoP, PA/ISI and any civilian who supports them is a crusader as its part of them and hence we can fight them.
For the simple mind its pretty straight forward. Whats valid across the border should be valid for Pakistan as well. If you check out Saleem Safi's recent JIRGA episode you will understand this conundrum of how "Islamic" politcal parties get confused when trying to justify their dual policies.