Zia has done several good things no doubt about that. Even his policy of getting engaged in Afghanistan was partially right for this gave him time and money and thwart the pressure of the West to get the nuclear program completed. However, his policy of allowing madrasas to grow like mushrooms, not curbing religious extremism, trying to implement religion at the state level, and letting Afghan refugees infest the country unchecked have done huge damage to Pakistan. There are always two sides of the coin and I have yet to know a person who is completely good or completely bad.
Regarding Qaadyanis... it was Bhutto who declared them non-Muslim and not Zia, that should get cleared. There were no persecutions of Qadyanis in Zia's time and I am a personal witness to that. There were several Qadyani officers working with my father and they got promoted etc and even reached to the ranks of Director General. Zarwan, I tell you one thing. Religion is one's very personal business. It should not bother you so long a person is serving his country and doing his/her job well.