State and religion were intertwined the day Pakistan was made. It was made because the Muslim minority in India had suffered under the Hindu majority's rule in the govt that was formed in British India in the late 30's. They were afraid of what would happen after the Britishers were gone and weren't there to limit the Hindus anymore. And that proved to be correct, in India every minority even big ones, like Muslims still living there and Sikhs, even lower-caste "untouchable" Hindus suffer brutally. Various sacred places of all these minorities have been torched to the ground, Christians were actually burnt alive in a famous incident.
Gen Zia is blamed for "starting this mess", "getting Pakistan involved in Afghanistan's problems". That is a silly point of view. Afghanistan has very few resources to offer, the real aim of the Soviets was to access the warm water ports of Pakistan. Many important Soviet naval ports were frozen much of the year and it was a major limitation for them. Rather than fighting a war for Pakistan's survival in Pakistan(fighting on two fronts is immensely difficult even for very well-equipped armies like Hitler's Germany - The Soviets were heavily arming Indos with MiG-25s and MiG-29s and other latest-gen armnaments to prepare for that two-front scenario, that Pakistan dreaded). Rather than fighting for Pakistan's survival in Pakistan, he chose to help our Afghan neighbors and fight for Pakistan's survival there.
People blame all this terrorism, bomb blasts and everything that's going on in Pakistan on Gen Zia. The fact of the matter is, the 90's were relatively peaceful and quiet. This terrorism only started when another superpower, the US this time, came over and squatted next-door. And now we're getting these well-funded and well-supplied terrorists crossing into Pakistan from Afghanistan again. They do things forbidden in Islam, that no good Muslim would ever do, like tricking 8-year-olds into carrying bombs, bombinb Mosques and places of worship, targetting women, children, and non-combatants. The Afghan Mujahideen never did this - this type of warfare is unprecedented in Muslim history.
The bottomline is that the US plays a very dirty game. They used Pakistan in the 80's, and imposed severe sanctions when they didn't need us anymore. And it looks like they're almost through with us again. When they were failing in Vietnam, they placed all the blame on neighboring Cambodia, doing all sorts of things to make Cambodia look unstable and then bombing "terrorists" in Cambodia for helping the Vietnamese who were beating the US. In this war, it looks like we are their "Cambodia". They are not a fighting army - they're full of High School students looking to go to college on the govt's dime, their media feeds them propaganda of glory and honor about how great the US army is. And then, in the battlefield they can't fight ragtag Afghans who have no airforce, proper army, and aren't even equipped properly.
That's what's happening in Pakistan today. Zia dealt with the US on even terms, they were not allowed to degrade Pakistan like this. This government on the other hand, the US facilitated their election. Current president couldn't even come to Pakistan because of corruption and embezzlement cases against him - he would have been sent to jail. So the US got Mush to "forgive" that, that whole NRO "National Reconciliation" trick, even Musharraf's folks say that the US pressured them into doing that. And then booted Mush out, as this government is even more pliant in front of them.