For the founders, protecting the freedom of religious belief was, first and foremost, an empirical assertion, on the level of the "self-evident" assertion of human equality. ... The Supreme Court has now said repeatedly that moral disapproval of homosexuality -- absent any compelling governmental interest such as protecting people from harm -- cannot be used to deprive people of liberty, including the freedom of consensual sex. Its decisions were not a matter of controlling belief, but of protecting universal freedoms against government incursions that were being justified solely by a belief in the immorality of homosexuality.
If you choose to run a business, organization or state (or country), you are signing up to play by a common set of rules. These rules should not be set by the mere profession of some people's beliefs, particularly when those beliefs are not subject to standards of empirical evidence about the costs and benefits of the policies they're cited to justify.
http://www.huffingtonpost.com/nathaniel-frank/belief-alone-is-no-basis_b_1326565.html