Churches that enjoy state support through their tax exempt status should appropriately be forced to give up their anti-gay disciminatory doctrines and practices, just as they were forced to give up their racial discimination during the civil rights era.
In several of the court cases I alluded to, churches who disciminated against gays regarding the use of their public facilities for weddings appropriately lost their tax exempt status.
In effect, churches that wish to hold on to a doctrine that violates the equal protection clause of the Constitution, as well as many state anti-discrimination laws, should lose their tax exempt status and become private, members only clubs. Otherwise, the state is complicit in a churche's disciminatory practices, in clear violation of the Constitution's equal protection clause.
The establishment clause was never meant to give religion carte blanch to violate the fundamental civil rights of its members. It has limitations, as it should. Non profit status may be appropriate for some churches, who, after all, occasionally perform good works and do not exist to make a profit (which, in so many cases, is complete and utter bullshit, but that's another issue), but only those who agree to comply with the highest law of the land.