As University of Chicago legal historian, Philip Hamburger, has shown in his history of the Separation of Church and State, none of the major framers favored Separation until about the election of 1800, when the Jeffersonians urged Separation to silence Northern clergy. Indeed, in the 1780s some religious leaders who were accused of wanting Separation denied such a misreading of their position. In the 1780s and early 1790s, a few religious dissenters favored Separation, but none of the insiders--certainly not Madison.Let me just add a little something. Most people know that the phrase "separation of church and state" is not in the Constitution. It was originally used by Thomas Jefferson in order to placate Northern clergy in his run for the Presidency. In its original useage, "the wall of separation between church and state" was there to protect the church from the state not the other way around.
What Madison wanted in the 1780s was disestablishment of religion and equal liberty for different religions, not a "wall of separation."
Another point is that when the constitution and founding fathers use words like "establishment" and "disestablishment" in relation to religion, they are talking about setting up or tearing down an official state church. They are not talking about scrubbing religious life from the public square completely or establishing what is essentially an athiest state. I'm willing to bet they thought the public dialogue of a democratic state should be representative of the political, moral, and religious values of its people.
I think the original meaning of both these phrases has unfortunately been lost.