If your organization does not support the right of gay men and women to marry, then the government should be very clear that you’re in the wrong. And it should certainly not bend over backwards to give you the privilege of tax exemption.
We have religious freedom in this country, and any religious organization is entirely free to espouse whatever crazy views it likes. But when those views are fanatical and hurtful, they come into conflict with the views of any honorable legislator who believes in freedom and equality. And at that point, it makes perfect sense for our elected representatives to register their disapproval by abolishing the tax exemption for organizations who cling to narrow-minded and anachronistic views.