Complex issues here. I can't speak for the US, but I know that in Canada the principle works along these lines:
Because Canada is a multicultural nation, its citizens comprise a wide variety of ethinc and religious backgrounds. You can't make political decisions based on Christian theocracy in a country that also has large Jewish, Muslim, Hindu, Buddhist, Atheist, and Native American communities (to say nothing of deciding whether the government's decisions should be based on Catholic, Anglican, Baptist, Methodist, Presbyterian, Mormon, Penetcostal, etc. etc. beliefs). While our democracy is indeed based on majority decision, we also feel a deep moral obligation to protect the rights of minorities from the abuse of power traditionally associated with hegemonic majorities (we did have a violent period in the mid 1800s, and again in the mid 1900s, as a result of "majority rules" politics).
Even in the early days, disputes between French Roman Catholic and English Protestant factions in government forced our leaders into the realization that determining anything legal that was good for everyone in the country couldn't be done if it was approached from a religious position. For that reason, religion was separated from state matters.
Matters like performing marriage ceremonies are considered civic, and not human, rights. Therefore, the concern over whether or not a same-gendered spouse has a right to inheritance or insurance coverage is a matter for the state. Whether the marriage ceremony is performed within a religious institution is left up to the institution.
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