In my humble opinion the world 'Secularism' is often taken as a misnomer and extrapolated to define things that are prerequisites for a Secular Democracy and yet wholly distinct - Pluralism and Impartiality ! Without them, Secularism is not possible and yet without a Separation of State and Religion, either of the two are very much possible.
As I have understood the Two Nation Theory to be is that it was an expression of us, Muslims, that because Islam, as per our believes, is a complete code of conduct for a believer, regulating everything from one's personal hygiene to Governance, we, Muslims, need a space to express ourselves, as per those beliefs. One would also do well to realize that it wasn't as if Jinnah dreamt up the TNT one evening and proclaimed 'Pakistan' the next morning; no, Pakistan progressed from constitutional guarantees to ensure that the Muslim vote isn't stifled by virtue of us being vastly outnumbered, to an amalgamation of Muslim majority provinces in the North and the North East (and Bengal) to form two federating units where we'd get to make our own laws to finally demanding for a separate Homeland.
I believe that both the Secularists and the Islamists are erroneous in their understanding of Mr.Jinnah and his conceptualization of Pakistan for one finds ample and incessant mention of words with a deeply, deeply 'Islamic' connotation in many of Jinnah's speeches; however similarly one finds Jinnah's vociferous refusal to let Pakistan be a 'theocracy' and instead a Nation where the 'Rights, Obligations and Privileges of all shall be Equal and Guaranteed' !
One may not look further than Jinnah's address to the State Bank of Pakistan (at its inauguration) and observe : 'We must work our destiny in our own way and present to the world an economic system based on true Islamic concept of equality of manhood and social justice. We will thereby be fulfilling our mission as Muslims and giving to humanity the message of peace which alone can save it and secure the welfare, happiness and prosperity of mankind.' The rest of the speech is riddled with talks of Islamic ideals as well !
A further example could also be his Dhaka Radio Broadcast of '48 in which he, after talking about the ills of Provincialism, goes on to talk about how '..You are voicing only my sentiments and the sentiments of millions of Musalmaans when you say that Pakistan will be based on the pure foundations of social justice and Islamic Socialism, not other 'isms' '.
And yet Jinnah's broadcasts to the people of the United States and of Australia, both in Feb '48, makes it very clear that though the vast majority of us are Muslims, 'Pakistan is not a theocracy or anything like it'.
His Pluralism and Impartiality is quite evident in his 11th August Speech (need I reproduce it ?) where he says : 'You are free; you are free to go to your temples, you are free to go to your mosques or to any other place or worship in this State of Pakistan. You may belong to any religion or caste or creed — that has nothing to do with the business of the State. As you know, history shows that in England, conditions, some time ago, were much worse than those prevailing in India today. The Roman Catholics and the Protestants persecuted each other. Even now there are some States in existence where there are discriminations made and bars imposed against a particular class. Thank God, we are not starting in those days. We are starting in the days where there is no discrimination, no distinction between one community and another, no discrimination between one caste or creed and another. We are starting with this fundamental principle that we are all citizens and equal citizens of one State.'
Furthermore, we often make this mistake of reading far too much into Mr.Jinnah's speeches without giving even a cursory look to Iqbal, who was no less integral to Pakistan's conceptualization. Iqbal, as I have understood him to be, writes in his 'Reconstruction of Religious Thought in Islam'; that after the emergence of the modern day concept of a Nation state, there has been an intrinsic shift in world dynamics which has influenced everything; the Hindus, the Christians, the Muslims etc., of yesterday where loyal to their communities and often at logger heads with each other but now they have something greater to believe in, something that allows them to transcend their bickering and allows them to act in perfect harmony with both their religion and their countrymen ! As such Islam too must reform, our perceptions must reform; the Hindu or the Christian of yesterday was a Dhimmi who may be more loyal or amenable to the rule of his fellow co-religionist then a Muslim Monarch because he couldn't truly own up to a Muslim Monarchy and vice versa for Muslim; but ever since this concept of 'Nationalism' we have the chance to create something that all of us can own up to and so our perceptions of how people of other religions should be perceived, dealt with and what kind of relationships to be had with them must evolve ! However for Islam to evolve we must give up this curse of Taqlid (or Imitation) that has crippled us into following an Islam that was more suited to medieval Arabia than the 20 th century. This, by the way, doesn't mean a Revision of Islamic values but simply a Revision of the deductions we made from Islam and so for that we need the Parliament, in Iqbal's words, to conduct Ijtihad (or consensus to form a legal opinion) to bring Islam to modernity !
Jinnah expressed his affirmation in Iqbal's point of view when he saidl, as per Hector Bolitho, the author of “Jinnah, Creator of Pakistan” : 'His views were substantially in consonance with my own and had finally led me to the same conclusions.' And those views, in my humble opinion were that we need a truly democratic homeland of our own where each community would have the right to practise their religion ! Where religious and legal pluralism will be guaranteed and yet complete impartiality will be maintained by those in charge of Governance ! How this is a bit different from 'Secularism' is that this allows for the Muslims (and the Non-Muslims alike) to express the communal aspects of their religion for example where Islam talks about formulating a system of Economics whereby Ri'bah or Interest (a certain kind) is taken out of the equation will be something that the Muslims can demand ! Whereas such a resolution, were it to be tabled in the Parliament of a Secular Democracy, would be declared Un-Constitutional by the Constitutional Courts ! Similarly if a Jew or a Hindu were to table a resolution in the Parliament with a distinct religious connotation it should be entertained ! The Impartiality aspect ensures that the right man, for the right job is elected or nominated; if someone like Justice (R) Rana Bhagwandas, a very capable jurist, is found to be equally capable for the Presidency of Pakistan....he should be elected to that post !
The reason 'Pluralism and Impartiality' instead of 'Secularism' would be more understandable for a Muslim majority state is because we, in Islam, have a profound and pronounced communal aspect to our religion; and certain things are made incumbent upon Muslims when they sit together and form a community of their own...enough to justify a political voice of its own ! And so it would be very hard for a particular Muslim to nod the head in the agreement when the Quran talks about praying 5 times a day or fasting in Ramadan but look they other way when the same Quran talks about what has been called 'Islamic Jurisprudence, Islamic Finance, Islamic ethics and consequently Standards of Propriety' ! A system that is truly democratic in its essence which allows for an expression of these 'communal obligations' and yet maintains a sense of 'impartiality' whereby no one is discriminated on the basis of their religion, is what, I believe, Jinnah and Iqbal wanted Pakistan to be !
Just my two cents !