Pakistan was not founded as an Islamic State. It was founded as a Secular Democracy for Muslims of India.
The constitution of Pakistan was secular. The Sharia was incorporated by Zia and his cronies.
Jinnah never once used the term Secular, did bend over backwards to emphisize that it would not be a theocracy (whatever he meant by the term), however did refer to Pakistan as a "modern" Islamic state (again, whatever he meant by the term). He dropped the "I" bomb many a times in his speeches, and I take his invocation of Islam as quite sincere...unfortunately I don't think he ever coherently formulated what this modern Isalmic state was...
As for being a secular state, Jinnah knew of Attaturk, and his secularization...and quite clearly rejected that extreme form of secularism. HIs own invocation of Islam clearly points to his rejection of any staunch secularism...
Pakistan was founded on a strange ideological principle, TNT, which did not spell out the characteristic of this Muslim state. I dare say, the distinction between Muslim state and Islamic state among those who mattered most, i.e. those who gave Jinnah mindshare in this thing he called Pakistan, was lost.
Between Iqbal and Jinnah, there is some concept of a state that is neither secular nor traditionally Islamic (i.e. nothing by way of an Ottoman-inspired caliphate, Islamic legal system and governance system, etc.).
The constitution, to my understanding, was not written during Jinnah's life...however Islamic provisions were introduced in the original 1956 constitution, essentially establishing Shariah as a prime source of law if not in practice, at least in intent. It was a this time Pakistan became, officially, a republic...indeed, an Islamic republic.