it was some judicial stupidity too. a large part of the argument made, and decision made, was based on 1/2 of 1 correspondence between jefferson and the danbury baptist church. it the entire exchage had been considered, there is no way they could have come to the conclusion they claimed. jefferson had a lot to say about government and religion and if they were going to use him as an excuse, they should have considered all his writings.
Here are a few.
I consider the government of the United States as interdicted by the Constitution from intermeddling in religious institutions, their doctrines, discipline, or exercises. This results not only from the provision that no law shall be made respecting the establishment or free exercise of religion, but from that also which reserves to the states the powers not delegated to the United States. Certainly, no power to prescribe any religious exercise or to assume authority in religious discipline has been delegated to the General Government. It must rest with the States, as far as it can be in any human authority (letter to Samuel Miller, Jan. 23, 1808).
To suffer the civil magistrate to intrude his powers into the field of opinion and to restrain the profession or propagation of principles on supposition of their ill tendency is a dangerous fallacy which at once destroys all religious liberty, because he being of course judge of that tendency will make his opinions the rule of judgment and approve or condemn the sentiments of others only as they shall square with or differ from his own (Statute for Religious Freedom, 1779).
We have solved by fair experiment the great and interesting question whether freedom of religion is compatible with order in government and obedience to the laws. And we have experienced the quiet as well as the comfort which results from leaving every one to profess freely and openly those principles of religion which are the inductions of his own reason and the serious convictions of his own inquiries (Letter to the Virginia Baptists, 1808).
Among the most inestimable of our blessings is that...of liberty to worship our Creator in the way we think most agreeable to His will; a liberty deemed in other countries incompatible with good government and yet proved by our experience to be its best support (Reply to Baptist Address, 1807).
and then there is that pesky thing called the cosntitution, which has no seperation of church and state in it, and it an instruction to congress, no more...no less.
1st amendment to the constitution:
Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances