It's good to see this kind of stuff. All wedding photographers should take note. Bad that it was posted on Gawker, and the rude, out of touch article that went along with this video. Point being...
ALWAYS talk to the person officiating the ceremony AND the bride and groom about their wedding photography. This is YOUR job as the photographer, don't leave it for the couple to deal with, and certainly don't wait until the day of the wedding to do it. Fact of the matter is, the church is a sacred place, and you have to follow the rules.
No flash is the only issue I've ever personally had to deal with, but most pastors are pretty liberal when it comes to photography and will let you do as you please. Obviously others, like this guy, have a different set of rules.