Delta,
While I agree with the gist of what you have said, I sense the implication that the 'average Pakistani citizen' (whatever that is) does not oppose the mindless barbarism of these militant groups.
Nothing could be further from the truth. Certainly there are those, as in any society, who delight in the misery of others, but to ascribe such views to all or most is erroneous, and I assume you are not going to be as shallow as Thomas Friedman to demand a literal 'protest' as evidence of 'opposition to fanaticism'.
The question here isn't one of the 'average Pakistani' renouncing fanaticism, it is about the State reversing past policies and enforcing its writ in its territory, strengthening its institutions and recapturing the faith of the citizens of Pakistan. Even in the most conservative and least developed parts of Pakistan, the North West, we have villages, towns and tribes rising up against the Taliban, as the military finally attempts to restore the governments writ.
However, to get to your larger point, I agree that the people who refuse to believe the atrocities ascribed to these militants, or justify them in various ways, need to realize that atrocities or not, the time for proxy wars is over, and as Asim and you stated, the only armed force on Pakistani soil should be the Military and law enforcement of Pakistan.