Jefferson wrote his one single reference about the “separation of church and state” in a letter to the Danbury Baptist church. He was writing about protecting religion from the federal government, not about protecting government from religion. Jefferson supported religious freedom and worked with James Madison in 1786 to write the Virginia Statute of Religious Freedom, which not only shut down official sanction of the Church of England but also prevented the state from compelling any citizen in religious activities. It blocked a plan to compel citizens to pay taxes that would then be used for any church activities.
What Jefferson was saying, that he had read from the Constitution, which had been written by his colleague of similar mind, Madison, is that the federal government has no authority to compell a church to do anything. It is separate and cannot compel a church to recognize and perform a gay “marriage” if it goes against the views of the church. And that the federal government is separate and is not authorized by the Constitution to force religious institutions to pay for abortions and birth control.
Jefferson got it. The Supremes didn’t. In fact, this is so far and away, so nearly the opposite of what the founders had written and allowed that one has to wonder why the question of disbarment has not been raised.