It is the opinion of Pakistani Intellectuals, Writers and Journalists Mr. Jinnah was a Secular reader.
My personal is:
“The secular intellectuals forward many political and legal arguments in favour of the lack of the courage of their Hero. The simple fact is that he did not declare Pakistan as a Secular State because he had some other vision. His hesitation is a sign of his doubtful sincerity in secularism.
The Secular Scholars cite very often the 11th. August, 1947 speech of Mr. Jinnah where he guarantees the complete religious freedom to the citizens of the state and declares that State has nothing to do with the religion. The problem is that it is only half definition of a Secular State. The other half is that �the religion has nothing to do in the state affair (the system of the government.)�. He always ignored this other half of the secularism. It is a clear indication that Mr. Jinnah wanted the religion in the state (Government) to govern the people in the name of Allah without the interference of the religious authority. He simply did not want �theocracy�. Perhaps he did not know it but he was following the advice of the other proclaimed secular philosopher Allama Iqbal “.

جدا ہو دین سیاست سے
تو رہ جاتی ہے چنگیزی

http://familyofheart.com/DOC/Current-posting/ahsan.htm

I also wrote:

“The Father of the nation of Pakistan Mr. Mohammad Ali Jinnah used argumentative logic (rational) in his professional life and in politics. But in his personal life he had a deep root of his religion (irrational). He got married to his Parsi wife only when she converted to Islam. He wanted her daughter to marry a Muslim husband and not a Parsi boy. It is certainly a conservative religious attitude and irrational.”

http://familyofheart.com/11/jan23/presentation-MAK.htm

You can always send me your comments to:

ahsan@noos.fr

Good luck.
Ahsan

You’ll be surprised that I do agree with what you said other than labeling Jinnah as “Secular” and many other past comments on same forum can help you to find out reasons.

Cheers.