I thought they were mostly connected to the politicians and that's how they managed to run and act as freely as they did.
That bold part is why I admire Musharraf. He had cleaned the ISI of such mindless fanatics, who had infiltrated deep into the organization and were often the source of one conspiracy or the other against the Pakistani state itself.
Well, not everything is hunky dory, but are things really as bad as you portray? For the way you state it, it appears beyond salvation, but I think it's not as bad. The Army, howsoever infested, will ultimately have to look for its own interest, and that can come only from an organized nation. If not today, then tomorrow, ultimately the Army will have to weed these elements out.