The courts are saying that a justice of the peace or other government agencies that can perform legal unions of two people can't prevent that union based on gender.
No one is saying, or ever said, that the widely accepted "mainstream" religions have to perform ceremonies for those that do not ascribe to that religion's tenets. If a church's definition of a union requires one from each gender, then those are their rules. Don't like 'em? Go to city hall.
The church is a substitute acting on behalf of the state to perform the ceremony. The state issues marriage licenses, the state may require blood tests, the state may require infectious disease tests before allowing any legal union. What's the big deal with having the state complete the work they start?
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