Naveed Ali has contributed the following rebuttal to Dr. Safdar Mehmood’s article “Did Jinnah Aspire to a Secular Pakistan” which you can read here
I again strongly condemn the notion used by Dr. Mehmood that these are atheists or anti-religious who talk in favour of secularism (and subsequently suggest that Jinnah was a secular and wanted a secular state) or that secularism is against religion or that being secular means being an atheist. These are basic misconceptions deliberately told to Pakistani public every now and then, matter of fact is that secularism goes hand in hand with democracy; it demands equal rights for all citizens so state cannot adopt a religious policy and it should remain neutral and shows no bias towards any religion. Certainly, all citizens of a state have equal rights, otherwise how will you ensure justice and provide equal opportunities to your citizens?
In Pakistan, a non Muslim cannot get commission in Army, you have to declare your religion on your Passport, a non Muslim Pakistani cannot hold many high level designations and there are many other examples which show a negation of basic human rights and equality by state under disguise of religion. Dr. Mehmood and like minded can come up with reasons, but all those reasons will be based on insecurity and fear. No nation can progress with insecurity and fear and prejudices.
Take state of Israel as an example, where religion plays an important role in state affairs. Can I ask if ‘anti-secular’ Pakistanis support state of Israel as a Jewish Democratic State? Can they see equal rights for Arabs (Muslims and Christians) in that state? Cannot they see that Israeli state supports a particular religion and has discriminatory policies against others hence against its own citizens? I hope it will be justified for anti-secular elements (as what you chose for yourself should be right for others as well) when PM of Israel proposed an amendment to the Citizenship Act, mandating that all aspiring citizens would be required to pledge their allegiance not only to Israel but to a “Jewish, democratic” Israel.
Basic flaw in political thinking and understanding of many Pakistani scholars is that they are insecure and inflexible because of incomplete knowledge and assumptions made by them to fill the gap in their knowledge; they try to interpret the world around them which is largely changed and progressed. The more it agitates them the harder they try to justify themselves and it results in distortion and narrow mindedness apparent in every walk of life in Pakistan.
Now coming back to Jinnah, we must look at his complete career from start to finish, in order to understand him better. We must acknowledge that fact that India and its political leadership were facing internal challenges of communalism, illiteracy and poverty along with imperialism, and it was a complex situation they were dealing with. Jinnah started his career in this scenario and gradually progressed, most of his career he tried to find common grounds for Hindu Muslim unity and later concluded that separation is a better path though he was fiercely opposed by certain sections of Muslim community.
Creation of Pakistan is not his achievement as events do not take place on will of a single person, there were many factors behind his success besides his own leadership and political skills, yet he has to be accommodating and flexible to get advantage from situations he find himself in. We must look at the context of his speeches; when, where and in which circumstances they were delivered and whom were his audience. He was manoeuvring with various interest groups and contrasting motivations and that is why he never clearly outlined the objectives of Pakistani state.
“The new state was meant to achieve different things for different people; emancipation from Hindu landlords for the peasantry of Bengal and Assam; creation of new economic and political opportunities for frustrated urban classes of Dehli, Bombay, UP and CP, and establishment of an Islamic state for religiously minded in Sindh, Punjab and NWFP” 
Importance of speech of 11 August 1947 is that it was delivered to the Constituent Assembly of Pakistan and it stressed on religious freedom, supremacy of law and justice and equality for all citizens of Pakistan. Founder of Pakistan was advising the elected members of first Constituent Assembly of Pakistan to follow these principles and these principles are secular in nature which of course comply to any religion’s teachings as well, because secularism is not against religion.
History has complexities, many say it was mere clever tactic by Gandhi to offer Jinnah premiership of united India, but imagine if it would have been done? We must also regard the fact how Jinnah is understood by those outside of Pakistan, despite what ‘conspiracies’ alike of Dr. Mehmood can ‘discover’. Following from L. K. Advani attest to what most in outside world understand about Jinnah.
“There are many people who leave an irreversible stamp on history. But there are few who actually create history. Qaed-e-Azam Mohammed Ali Jinnah was one such rare individual. In his early years, leading luminary of freedom struggle Sarojini Naidu described Jinnah as an ambassador of Hindu-Muslim unity. His address to the Constituent Assembly of Pakistan on August 11, 1947 is really a classic and a forceful espousal of a secular state in which every citizen would be free to follow his own religion. The State shall make no distinction between the citizens on the grounds of faith. My respectful homage to this great man.” 
This is a continued debate between two contrasting viewpoints in Pakistan whether Jinnah wanted a secular or a theocratic state? Importance of this debate lies in the fact that both groups suggest a different solution to the challenges faced by Pakistan today. Qauid-e-Azam is important for both of them as a leader who is admired by the nation and hence his portrayal under one or other framework can benefit them. It is however on us to understand what the best course is for future of Pakistan. What is choice for ordinary Pakistani? It is to understand that where they want ‘their’ Pakistan to be, they can take inspirations from past and learn to not commit the mistakes made by their predecessors. Pakistan was not only Jinnah’s; it was and it belongs to us, millions of Pakistanis, and we have to be intelligent and progressive enough to decide our fate. And it is also on us how we understand our Quaid-e-Azam, our fate will not change the fact who M.A. Jinnah was. End of the day, it is now on us to lead Pakistan, to success or destruction.
 Shahid Jawed Burki in “Pakistan: The Continuing search for nationhood,2nd ed. p22”
 L. K. Advani wrote this on his visit to Jinnah’s Mausoleum, http://en.wikipedia.org/wiki/Muhammad_Ali_Jinnah%27s_11th_August_Speech