There have been two conflicting traditions in the United States about the relationship between church and state. The first is exemplified by the holiday of Thanksgiving, which emphasizes the religious foundation of the United States. The Pilgrim fathers set out in the New World not only to worship as they wanted but to establish God's kingdom. They had the truth and all others were wrong; church and state were one. The second tradition comes from the time of the writing of the American Constitution, when our deistic, freethinking Founding Fathers (no mothers) embodied in the Constitution the principle of separation of church and state.
Here's a section that drew my attention:
The general pervasiveness of Christian assumptions about morality and family was reinforced by the so-called Mormon cases, the first of which Reynolds v. United States, which reached the Supreme Court in 1878 and established monogamy as the norm, ruling that it was the basis of Western (read mainstream Christian) societal life. In a sense, this was a double-edged decision because the Justices, in their effort to outlaw the Mormon practice, in effect asserted that marriage could be regulated by law, guaranteeing the states the right to issue licenses and to control marriage independent of the church.
Another one of the Mormon decisions marked the most far-reaching secular claims of government. The case of the Church of Jesus Christ of Latter Day Saints v. United States (1890) upheld the constitutionality of a law adopted by Congress in 1887 that annulled the charter of the Mormon church and declared all the property forfeited except a small portion used exclusively for worship. In a sense, however, this case represented not so much a conflict between church and state, but a statement of the dominant religions in United States against the feared Mormons.
The way I interpret the decision is that the Court was able to assert the supremacy of state over church because it was basically concerned with what Mormonism was doing to good Christian belief, and in this it had the almost unanimous support of all the other churches in the United States. In fact, as late as United States v. MacIntosh (1931), the Court went so far as to declare that Americans were a Christian people. The actual case dealt with a conscientious objector who had applied for citizenship and been denied. He appealed, and the Court decided that, unless Congress ruled otherwise, obedience to the laws of the land was required since such laws were not inconsistent with the will of God, i.e., as interpreted by mainstream Christian thinkers.