Not really sure. My guess is that many Pakistanis have been immersed so much in "religion" for so much of their lives - even at times they don't want to be - that they forget there are men who act in the genuine belief that they are acting in service of G-d, not selfishness.
The reason why I call attention to what should be an obvious point is that if this is the case there is a better way to address their issues than brute force alone: genuine and public dialogue. Find out what these mullahs' personal fears and aspirations are and define limits so they can pursue a meaningful life without imposing themselves upon the larger society and alleviating their perceived threat of the larger society imposing itself on them.
If after that they persist in attempting to destroy the State then you know they're not in it for a higher purpose, yes?