Dude, round truths are whole lies.
a) Neither Jinnah nor his counterparts on the Indian side truly wanted independence, but equal rights withn the commenwealth as subjects of the Queen. Jinnah was setup to be a Governer General…not a prime minister, nor a President. Opposition of the scholars should be taken in this light. OF COURSE their tune is going to change when Pakistan as an independent nation became a reality.
b) Jinnah had made reference to an Islamic state, but denied he wanted a theocratic state. Other idoelogues equally important to the Pakistan movement, e.g. Iqbal, definitely wanted an Islamic state. Nobody wanted the Mullahs to rule. If that is what is meant by “non-theocratic”, then yes. Jinnah did squat to squash Shariah-compliant, and Shariah-based legislation, which off the bat eliminates the possibility of Jinnah as an exponent for a secularized Pakistan.