I know that this is a bit of a duh post, but it must be emphasised that the Pakistan military must not become involved in choosing winners and losers in the civilian Pakistani structure. The situation is slightly better than the nineties, where the military was involved indirectly in kicking out three civilian setups and then in directly ousting a fourth government.
Right now of course, the military is not interested in directly running the country, maybe we can hope that some realisation of their limitations in power are entering the officer corps mind, but rather in influencing select sections of policy. Those select sections of course being defence and the country's relationships with India, Afghanistan and the United States.
To influence these factors the military uses its media tools, who openly parrot the military's line, the worst offence being during the Kerry-Lugar bill negotiations; negotiations that had been turned into a crisis for no discernible ends. The furore created over that bill was not just about destabilising the government just to show "Who's boss", may or may not have been about scuttling the damn thing, but it showed that the army does things utterly impetuously without thinking the consequences through to the end. What if the Kerry-Lugar bill is scuttled and you've shown the civilians "Who's boss?". Then what? What about the money to run the country? What about mending relations with the other non-Republican faction of the United States government? What about not giving in to your various personal insecurities and prejudices and thinking about the lives and securities of the People of this country? And yes the people of this country....the rather battered people of this country.......they relate to the human velociraptors sending out suicide bombers throughout the land. These are the fringe of the military's "civilian partners". The terrorists. The Islamic Extremists. The unelectable trained killers of the Lashkar-e-Taiba, Harkat-ul-Jihad-al-Islam, Harkat-ul-Islam, Harkat-ul-Mujahideen, and all the other aging Jihadis of the nineties, with nowhere to go and a crop of young, eager, willing to die kids coming up, and nowhere to send the psychopathic little fuckers.
So obviously the enterprising anti-government Jihadis of the Waziristan have put out the all points bulletin for any young Muslim with a hankering for God and Guns, who was raised in an environment ready to kill Indian (read Non-Muslim) soldiers, but has found the Pakistani government unwilling to send them across into Kashmir. The setup across non-Frontier Act ruled Pakistan is still there to bring up the next crop of Jihadis, the local police has been too slow, too weak, or too hampered from stopping the cyclical rise of a new crop of violence prone youngsters. The military protects the Punjabi ones who still promise to "eventually get to Kashmir". In the meantime, the young ones head up to Afghanistan independently. They then become more sectarianised and decide that it's time to purify Pakistan too. Some people begin to feel that it may be time to round up these groups, but have they become too evolved, too large, or too organic to uproot? The military still thinks it can use some of these people, if not for external warfare, then maybe to intimidate various local politicos, if the times require it. And the local violence machine keeps humming along as usual.