Our Founding Fathers understood that religion was an important dimension to liberty. Liberty values diversity, while tradition defines to unify. The Founders did not have one interpretation as to their religious understanding, when they founded our country. But, they did understand that an appeal to natural rights was necessary for the right to dissent. Natural rights were granted by "universal order", because God was the ordainer of such rights, not the government. Their "new experiment" was a "moral government" that protected and provided for liberty against power, position and might.
"Universal order" today, underwrites social Darwinism, the power and right of the "fittest". Today, Science defines to unify, as Tradition once did. But, the basis of such unity, structures society after power and not liberty, just as it did in pre-modernity.
Liberty of conscience in regards to religion was to protect against abuse of power in the Founder's eyes. And the structuring of "moral government" was a balance of power, not power itself. The law was the "ruler" and balancer of power.
Today, those that adhere to a politicized religious conscience can do so and should, but should not enforce their position upon those that "see" things differently. The sects are alive and well, which will continue to further bring alienation of such sects from the "Mother" Church Tradition or its Jewish root. But, each and every sect is an attempt at defining religious conviction, and defining commitment. Problems arise when these convictions and commitments impinge on another's right to liberty of conscience, opinion and commitment.
We must remember that whenever one defines, one also limits and judges. And yet, definitions are necessary for understanding and maintaining "order". Our Founders defined liberty according to the Constitution. The Constitution was to protect citizens from abuses of power. And our courts are the ones that will settle disputes of definitions.