Unfortunately he is right. Thomas Jefferson was an admitted deist and more than likely atheist. His idea of separation of state and church was the opposite of what is now believed. We think religion should not be in government. He thought that government should not be in religion.

Let's look at it his way. The government is made up of people. People have religious views even if it is atheism. People in government make decisions based on moral, ethical and religious values all the time even for very minor issues. If there is one just one person working for the government that is in any way religious their religion will have an affect on their decision making. It is impossible to have no religion in government because the government is made up of people. So now we have to look at how those decisions affect the government. Are they actually making laws or regulations based on their religion that effects others or is it something like praying during a smoke break? If it does effect others we need to take a close look at it to protect every ones freedom. It the nature of the beast, a constant battle.

He believed that if people in the community wanted to build a monument to budda that the government should not interfere with that decision. This did have ulterior motives. He lived among very religious people and wanted to ensure that the government also did not make anyone worship any gods thus protecting those who were not religious. He had to throw out the idea of freedom of religion to set the ground work for freedom from religion, he just could not come out and say it in the open.
The separation of church and state is not part of our constitution no matter how much we don't like it. It is an operational principle that exists in our government that is not part of our government.

Eventually, a supreme court justice made a decision and sighted the separation of church and state. That ruling became law and set a president, since then other rulings were based upon that decision and the idea has become Judicial but not Constitutional law. We really need a Constitutional amendment that will remedy this embarrassing and unfortunate oversight. The problem we will run into is, this country is still primarily Christian. If such a law was written it will likely somehow favor Christianity.