It's a subtle distinction but logically it's a valid one; you can't really argue against it without arguing against religious freedoms.
Now... do I think it's fair or right? That's a different debate - I absolutely don't - I abhor religious nonsense BUT if it's "a thing we respect" then we unfortunately can't pick and choose, and I do know that many religious people who have no issue with homosexuality and same-sex couples and unions are still against same-sex marriage.
Should they be? No, it's daft. But religion is daft.
what can you do really.