Jefferson clearly stated repeatedly that he intended a wall of separation.
Thomas Jefferson, as president, wrote a letter to the Danbury Baptist Association of Connecticut on 1802-JAN-1. It contains the first known reference to the "wall of separation". The essay states in part:
"...I contemplate with solemn reverence that act of the whole American people which declared that their legislature should 'make no law respecting an establishment of religion, or prohibiting the free exercise thereof,' thus building a wall of separation between Church and State..."
During the 1810's, President James Madison wrote an essay titled "Monopolies" which also refers to the importance of church-state separation. He stated in part:
"Strongly guarded as is the separation between religion and Government in the Constitution of the United States, the danger of encroachment by Ecclesiastical Bodies may be illustrated by precedents already furnished in their short history."
The US Supreme Court has interpreted the First Amendment as if it requires this "wall of separation" between church and state. It not only prohibits any government from adopting a particular denomination or religion as official, but requires government to avoid excessive involvement in religion.
http://www.religioustolerance.org/scs_intr.htm