One of the brilliant aspects of the Founding of the United States was its secular nature. Having known enough history to understand what happens in theocracies where government is based upon religion and not reason, they wisely separated Church and State.
One is free to believe and act as one wishes, but we have laws forbidding actions that would violate Rights. I may believe I should kill all the members of some group; but to act upon that would bring the full weight of law to curtail that action. The members of a group are free to believe, and practice, whatever they want. The only restriction is if such practices violate the Rights of others. Yes, religious "intolerance" must be tolerated.
Curiously, the term originates from those outside of the group labeling their own displeasure regarding the members of that group; no one within a group would consider their beliefs and actions intolerant.
Just because polygamy is illegal does not mean it is not practiced in Utah, where the state more or less turns a blind eye. Although the rest of the nation may balk, so what? Unless an individual's Rights are being violated, those who believe in it should be allowed to practice in peace. Although others may be "morally outraged," they who don't believe in it are not compelled to practice.