I take many Wedding Photos every year and I've been doing this for a long time....
I made it a habit a very long time ago to ask the Pastor, Rev., or who ever is giving the service if I may take photos during the service... The answer is every time.... NO.... But.... I then say how about if I use NO Flash? They almost all say that would be fine. They also point out to stay in the back, make no noise and do not disrupt the service... The only Church I have ever had trouble with is the Catholic Weddings because they do not even want to hear the shutter go off... But.... At most Catholic Churches there are Balconies and that is where I end up... No one sees me, no one hears me....
Of course taking pictures during the ceremony means very low light conditions, with no flash... High ISO's, bump up your exposures and take more than you would than with a flash...
The number 1 thing to do is ASK before you take..... You will notice others taking pictures during the service but that is their problem getting caught because you have permission...
I have not done a wedding yet without taking pictures during the Ceremony and I've been doing this since 1982...
Ric
PS. In my opinion this is the Bride and Grooms BIG moment and if they want the memories of the service they should have it...