Folks who argue for the left on matters of separation of church and state proudly point to Jefferson, who have us that little metaphor. As I have pointed out, Jefferson wrote the Declaration of Independence, but was not present at the time the Constitution and Bill of Rights were ratified. He was in France. He wrote to the Founders with opinion and advice, though. In those letters he did not use the phrase "separation of church and state" but rather used the phrase "freedom of religion." No matter. People who believe the whole "separation" idea as it has been applied by recent courts will largely ignore Jefferson's actions and word that might argue against the kind of separation the courts have mandated today.
It is instructive to look at some of Jefferson's other writings regarding the way we have allowed the courts to become the "last word" on the Constitutionality of laws and actions. He spoke often about the danger of the judicial branch if they chose to take on too much power. He clearly thought they should have no more power than the other two branches.
He also thought that even the federal government as a whole could not be the last word. If the feds take on too much power or overstep their boundaries, the states and the people still have the final word. We are a government of the people, by the people, and for the people. Remember in the New Testament how Jesus said that the Sabbath was made for man; man was not made for the Sabbath. In the same way, the Constitution was made for the people, not the other way around.
Below is a link to an article that examines Jefferson's Kentucky Resolutions of 1798 and the concept of nullification of federal actions. It is not very long and makes for interesting reading:
Courts aren’t the final arbiter