If they are running their chapel as a commercial enterprise they will be subject to such non-discrimination enforcements in many/most jurisdictions. Refusing to perform on the basis of their religious convictions is all good and proper, but religious freedom does not extend to a for-profit enterprise that serves the general public in most instances.
As businesspersons, one way they could deal with this is to have ready a hired gun minister whose principles differ and who is willing to come in and do the dirty deed - for pay, of course.
