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In my earlier studies of the etymology of "Separation of Church and State" I found its origins to lie 100-200 years before the Continental Congress. Much of the principal is based upon an assumption that identified morality with men who had a belief in God. The more mature that belief, the more studied one had become in the Church or Judaeism.

Judaism is a fundamental basis to Christianity.

All others are grouped generically as heathen or those guided by lusts and immorality. Pagan and unbelievers are understood to comprise a group not guided to respect morality.

The Separation of Church and State assumes this as premise. It then recognizes tht moral men will seek to obey both the laws of man and the laws of God. Recognizing immoral men will week to obey neither, the principal of Separation of Church and State is irrelevant to the governance of immoral men. Laws on criminality are their domain. Instead the Separation was simply focused on how moral men might reasonably govern themselves.

Moses had appointed lessor judges to assist him in adjudicating the law. There were laws of God provided in Scripture, but also other methods of governance man-made, which assisted God-fearing men in bearing their burden.

From the Inquisition onwards, political thought recognized the impact of the Church as a political force, yet also recognized the rights of the individual. Again the focus was on the moral man. Not the immoral, simply because no amount of legal ethic will suffice for the immoral man because he is rebellious to ethic regardless.

It was only in the last 30-40 years in American jurisprudence that the Separation of Church and State has been demphasized and freedom of religion differently identified to ANY spiritual pursuit.