Whose side is the Pakistan army on?

The Washington Post reports today that another U.S. missile strike in North Waziristan killed 5 militants, including an Al Qaeda operative Rashid Rauf, who held dual Pakistani and British citizenship:

Before his arrest, Rauf's ties to the Pakistani terrorist group Jaish-e-Mohammed stirred strong suspicions among intelligence experts that he may have also had connections with rogue elements within Pakistan's Inter-Services Intelligence Directorate, also known as the ISI. [...]

Suspicions about Rauf's connections to Pakistani intelligence agencies deepened after he escaped from custody in December 2007. [...]

Rauf's attorney at the time, Hashmat Habib, claimed Rauf was subsequently taken into ISI custody. Until Saturday's strike in North Waziristan, Rauf's whereabouts were not publicly known.

(full article here).

So let me get this straight: this guy was connected to the ISI, the ISI may even have had him in custody, and yet he was with fellow extremists when he was killed.

Whose side is Pakistan on, anyway?