Those churches and synagogues that do prohibit photography during the ceremony are most often trying to protect the sanctity of the ceremony itself so ultimately they do have your best interest at heart. It can be a difficult pill to swallow when you believe you are to have no images of the actual ceremony. Although our goal as photographers is to surpass your expectations and deliver to you precious images of all your wedding memories, it can create a difficult juxtaposition for us to disregard the rules that govern our presence at your wedding. As a business we want to earn their trust while keeping our promises to you. We want to be welcomed back again to their facility and not develop a reputation of disrespecting their wishes.
Technically, nowadays we are better prepared then ever before and most professional wedding photographers should be more then capable of delivering to you images taken during your ceremony. Remember to talk openly about your concerns with your photographer if you discover your facility has rules that govern photography. Ask them several questions about their cameras' capabilities and their own skills in low light situations. They should eagerly be able to answer your questions and alleviate your concerns. Its also a good idea to ask to see prior ceremony shots possibly taken at your location.
If your photographer is capable of handling low lighting and has experiences abiding by the rules then you can relax and trust that at minimum you should come away with several images of your ceremony. In the end you will find that for the sake of the album and story telling all you really need is a select few and that there is no real need for your photographer to become a distraction trying to get the perfect shot during your wedding ceremony. Educating yourself about the rules and insuring your photographer has what it takes can mean that the facilities' rules are respected but you do not have to be disappointed later.