Well, in my personal opinion the demand for Pakistan had major reasons of political, economic, social & cultural. Not the religion alone.

It is very much true that the Muslims & Hindus were 2 different civilizations. Civilization include a lot of factors, out of which religion is just one of them, not the only one. But the numeral majority, attitude & atrocities of Hindus was the real problems.

I would like to quote Sir Razi Abidi's words:
"Most the candidates in their papers use the word Islamic states. In reality there is no state in the world that is Islamic, all are Muslim states. Religion is a very personal thing. Our knowledge about the religion is superficial & all we know are the loud sermons of medieval scholars (Mullahs)."

I want to ask the question which also appeared in 2007 Pak Affairs paper:
Q. Elucidate Ideology of Pakistan. What are the reasons which contributed for the development of two-nation-theory? Is two-nation-theory relevant after the fall of Dacca? Discuss.

I'm unable to answer the part of the question "Is two-nation-theory relevant after the fall of Dacca".
If u think that religion was the binding force then y it seriously fell during tragic separation of 1971. Here, the major concerns were again the same as pre-1947. For example:
1. Denying to grant Bengali language the status of national language (remember Hindi-Urdu controversy)
2. Abstaining the one-person one-vote (as the East Pak had population majority)
3. Concentration of political power with the West Pak.
4. Non-industrailisation of East Pak & using it as raw material provider.
5. Non-representation of Bangalis in country's main stream.
5. Military operation & indulgence of some army officials' activities like..... (u must be knowing them)

Apart from Indian provocative through Mukti Bahini y a new country was carved out despite of having the same religion?? Y religion could not make them consolidated.