To be fair, Jefferson DID mention the words "Separation between Church and State" when addressing a Baptist Congregation once, to reassure them that the state would not try to dictate what they could say.
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.
Christian Antagonists love to quote the first part of that "no law respecting an establishment of..." but ingnore the "or prohibiting the free exercise of" part. It was meant to protect religious freedom, not to remove religion from society. The intent was to protect churches from the meddlings of the state.