The founding fathers had no desire for religion to be involved in the Federal government. However, they were ok with the STATES establishing religions. In fact the famous letter from 1802 written by Thomas Jefferson to the Danbury Baptists, from which is derived the doctrine of separation of church and state, was a response to a letter from the baptists in Danbury Connecticut complaining about the state religion of that state: Congregationalists. Jefferson's response did not say the state could not establish a religion, only that the Federal government could not. Many states had official religions well into the 19th century.
Do I want to go back to that? NO. But to say that the founding fathers were against religions having a role in government is only partially true as they had no issue with the states establishing religions.