Respect the event for what it really is. Two people are committing themselves to marriage and making binding vows to that effect. The family and guests are there to see the bride and groom as they pass through the celebration of this event. They want to focus on the two most important people, and the actions of the photographer should not distract their attention. Photography is just a desirable but optional extra.
Agree in advance what movements you intend to make during the service or ceremony, and move as quietly and unobtrusively as possible. Try to avoid using the central aisle in a church - there may be other routes you can use at either side. Also remember to set up a tripod shortly before the event so that noise is kept to a minimum. Turn off your mobile phone and also any sounds made by your camera. Electronic beeps are best avoided when vows are being made.
Finally, in the case of a religious service, respect the beliefs of others. Whatever your own faith, or lack of it, recognize that there is likely to be every shade of opinion within the assembled guests. A photographer who respects the views of others, and achieves the required results as unobtrusively as possible, will gain the respect of everyone who attends the wedding.