Interesting to know that you are on active service. No wonder you are so composed even when speaking to a lot of amateur defence enthusiasts online. I am not very knowledgeable about the intensity of sectarian violence in your country, though they seem to be quite unsettling from news reports. What startles me is the limited response of your civilian government compared to the eagerness of your armed forces to quell this threat.
Is this primarily due to political involvement of far right political parties? Because whether having any political stand, by slowing down your military's response to these militants, these parties are only making it worse for your own nationals. The coming decade is going to be extremely crucial in terms of how your government and armed forces tackle these militant organizations and their moles in some of your official positions who try to undermine the security forces' efforts. The sectarian disruptions as you mentioned, are just a kind of time borrowing process for regrouping and re-arming once sufficient resources have been availed for continuing their efforts. I would be of the opinion to move your forces to open up military-sponsored schools in very underprivileged regions where children are taught to be constructive and productive to the nation instead of allowing themselves to be carried away by militant ideologies.
That education especially when provided to youngsters between 8 to 20 years age can have tremendous impact on changing the course of this war in the coming decade. Since your government does not seem to be finding any right corners to turn straight, I think the onus is simply upon your armed forces to demand more funds for non-combat operations such as opening up schools and seminars for young children to be taught national dedication and proper non-religious education of science, business, mathematics and other such matters which will totally subdue any budding militant tendencies in the youth at an early age.
As much as I hate to undermine free democracy when compared to military rule or dominance, there is very limited option and very limited acting bodies other than armed forces in your country at the moment that can take visible steps to win this was psychologically first. A psychological victory gained right now by pushing youngsters and teenagers in rural and semi-arid areas away from religious fundamentalism would automatically mean having won half of this war.
The militants would be dry of potential fresh recruits leading to distrust and warring among themselves, gradually making the job of your security forces easier.
I know Pakistan is a conservative society, but separating religion from studies and common thinking is the only way left. The idea of keeping religion as a private communication between oneself and God and not to be brought out of the four walls has to be encouraged to allow modern and open thinking among semi-literate and rural population.