There is no denying that the religious leadership at the time of partition was an ardent opposition to the idea of Pakistan. Reasons for that however, are not clear, the most common view is that, there is no room in Islam for creating a land on the basis of "Qoumiat". This is followed by the notion that, since the Muslim League was primarily, an elitist party at the time of its inception,and did not represent the Muslims of India,has no right to speak on behalf of the Muslims, and thus should be opposed.
The second theory seems more plausible since the first one can easily be debunked wit the logic that,Muslims wanted a separate land because they were Muslims, and hence different.Our distinction, was in being Muslims, Jinnah always held the view that Indian Muslims are different than the Indian Hindus in many ways.The whole premise of partition revolves around religion, nationalism came into the picture much later.
The second theory is also a strawman's argument because ML was able to gain support of the majority of the Indian Muslims,making it the flag bearer of the Muslim's rights in India.This should have been enough a reason for the religious parties to slant in the favor of Jinnah and the ML, but that was not the case.So, on the charge of JI opposing the idea of Pakistan with all its might,they are guilty as charged.Only God knows, if their hearts have changed or not.