Yet they managed to run their own private agendas! haha! As of now, Musharraf's nephew Taj is running the ISI, speaks alot about how things are run there. Even now the whole worlds pointing fingers at them for the Indian embassy attack, amidst the double sided games the ISI is playing, and our Govt is clueless as to whats going on.
If Musharraf's own nephew is running ISI, and if his nephew has no will of his own (unlikely, as he must have been competent enough to be promoted on his own far enough even before Musharraf became COAS) and is just acting out Musharraf's instructions, that would do nothing but strengthen my case that the ISI is an extension of the military.
Whoever heads the ISI is free to shake things up and remove anyone known to be operating rogue.