Overread is right.... It is his church and most photographers I have seen do their best to work within their comfort zone. This includes bringing the parties together prior and discussing what is permitted and not permitted. Remember, religious marriage is a privilege extended to the couple by permission of the church. The church is NOT the bride and grooms servant or hired service. This is a holy church not some paid chapel in Las Vegas.
One wedding I shot did not allow ANY photography during the ceremony... it was considered disrespectful. The head photographer worked it out with the church to finish the ceremony without cameras and then perform a reenactment afterwards. It actually worked out wonderfully as the photographer had full control during the reenactment and even was allowed to set up some lighting (umbrellas and strobes).