Jinnah was a man, he was not an infallible being. His ideas and beliefs changed and shifted throughout his life, which is why everyone from communists to secularists and Islamists will quote him to support their beliefs.
Nor does it really matter, a country that tries to model it's political ideology strictly upon the diversely interpreted beliefs of it's founder sabotages itself of progress.
The issue with the debate in this thread is that there is a perception that Islam poses a threat to our ethnocultural/regional identity or that our ethnocultural/regional identity poses a threat to our Islamic identity, that there has to be either one or the other. That is simply not true, neither was Pakistan solely founded upon Islam as one side claims nor was Pakistan founded to be a secular state.
To address both sides here:
Pakistan was never intended to be based solely upon Islam nor is such an identity even feasible, as the separation of East Pakistan highlighted. Choudary Rehmat Ali, the original founder, first began to conceive the idea of Pakistan as a pushback to what he perceived as a British attempt to "Indianize" and erase the distinct ethnocultural identities of the peoples that comprised what is now known as Pakistan.
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"India, constituted as it is at the present moment, is not the name of one single country; nor the home of one single nation. It is, in fact, the designation of a State created by the British for the first time in history. It includes peoples who have never previously formed part of the Indian nation at any period of its history, but who have, on the contrary, from the dawn of history till the advent of the British, possessed and retained distinct nationalities of their own". ~ Now or Never, 1933
"The congress had designated all British possessions in South Asia as India denied to the non Indian nations the right to their own nationhood, and, by making pretentious claims, stamped Indian nationality on the peoples of this area." ~ What does the Pakistan National Movement Stand For? Pamphlet, 1930's
"That is, the statement which was to save us from national self-destruction on the altar of "Indians", safeguard our right to distinct national existence, mark the appearance of a de-Indianized Muslim country of nearly 35 million people, protect the heritage of the first three centuries of our history, inflict the first decisive defeat on the forces of "Indianism", and last, but by no means least, alter forever the course of the Millat, of Dinia (South Asia), and, I dare say, of Asia." ~ Ch, Millet and the Mission, 1930's
"This mistake has certainly cost us dear. It has compromised our nationality and labelled us all as "Indian". I say this, not because there is anything wrong with the word "India" which, in itself, is perhaps as respectable as any other name; but because we are not "Indian" and, therefore, for us to style ourselves or our institutions "Indian", is nothing but an act of renegation." ~ Ch, The Menace of Indianism, 1930's
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It is also often claimed that the idea of Pakistani identity incorporating aspects of it's native culture, heritage and history as a recent development is also false. Choudary Rehmat Ali drew heavily upon Pakistan's both pre-Islamic and Islamic heritage as among the basis for Pakistan and it's identity.
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"It will therefore be seen that Pakistan is one of the most ancient and illustrious countries of the Orient. Not only that. It is the only nation in the world which in the antiquity of its legend and lore, as in the character of its history and hopes, compares with Iraq and Egypt -the countries which are known as the cradle of the achievements of Mankind." ~ Fatherland of the Pak Nation
"It must be remembered that, in different periods of its life, Pakistan has had different names -names whose very variety epitomizes its past history, just as its present name symbolizes its present position, its future prospects, and its ultimate destiny in the world" ~ Fatherland of the Pak Nation
"The Mihran, also known as the Indus, is the longest, the greatest, and the most truly national river of Pakistan, and its course lies through most of the provinces of the country" ~ Ch, Physical Features
"In their origin the Paks belong to the stock from which sprang those gifted tribes of the pre-historic times who created and developed the oldest civilization of the Mihran Valley and, for that matter, of the world." Ch, Ethnical Stocks
"Pakistan, as already mentioned, was one of the three civilized regions of the globe~the other two being Iraq and Egypt. This fact stands out prominently against the dim hack-ground of that still ill-defined period in the growth of the human race. It shows that, in pre-history, Pakistan was one of the lands where civilization was born; where Man made
his first attempts at courting Nature for his subsistence; and where he achieved his first successes in his elemental struggle for life." ~ Ch, National Story
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It is also made clear in the Pakistan Declaration, that religion is one of three pillars (and not the sole pillar) for the foundation of Pakistan:
"I am enclosing herewith an appeal on behalf of the thirty million Muslims of PAKISTAN, who live in the five Northern Units of India--Punjab, North-West Frontier (Afghan) Province, Kashmir, Sind, and Baluchistan. It embodies their demand for the recognition of their national status, as distinct from the other inhabitants of India, by the grant to Pakistan of a separate Federal Constitution on
religious,
social and
historical grounds." ~ Pakistan Declaration, 1933
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However, that is not to say that Pakistan is independent of Islam as shown in the quote above.
We do not base our values and laws on what old white men think is right or wrong. Our values, laws and rules of governance are clearly enshrined in the Quran and Hadith, it is a system that all Muslims should strive for. To claim that our problems are the result of political Islam is nonsense considering that our laws and governance are already based on Western values and we are only Islamic on paper. Coming from someone that once completely embraced the ideas espoused in this article, I see Islam and Islamic governance as the only antidote to our political and social troubles, without it, we will always be in strife.
If one claims to support democratic values, then they should concede the fact that Pakistanis overwhelmingly desire Islamic law and governance.
He wanted investment in science, technology, education, education for both sexes, rights for the weak, non Muslims, animals
How would an Islamic state contradict any of this?