Even though your wedding has come and gone, I'll still share my two cents.
Most important thing to do is bring back up camera. God forbid something happens to your camera you'll sill be operational.
And I have to disagree about checking with the minister before hand about restrictions. If no one imposes restrictions on you without you asking them, then just do what you need to do to get the best photos you can. You know the old saying "its better to seek forgiveness than ask permission"? Its better to GET THE SHOT and piss someone off, than be a good boy and miss your opportunity. You are the photographer. So what if they get mad?? (the officiant, not the client). They are not going to make you delete that great shot you took against the rules. And I'm sure your client will thank you for it. I know *I* would rather hire a photographer who is willing to do whatever he has to to get the shot. Thats the difference between a pro and an amateur. Pros go above and beyond. Yes, I realize your not a pro, but in this situation you are taking on the role of the pro, so it still applies
Remember, the awkward situation is temporary, the photo lasts forever.
Plus, ive NEVER shot anywhere that didn't let me use flash. NEVER. ever. I've been shooting professionally for over 5 years. I don't know what these people are talking about who say MOST venues don't allow flash. So do what you must to get the photo and plea ignorance to get the angry venue workers to go away.
And if you do get harassed by a venue employee, just ignore them. They don't know your workflow or style. I was "yelled at" by an employee at a venue for eating at the same time as the guests. She wanted me to let the guests eat first because it is more "professional" to let them go first. BULL. I need to eat first so im not stuffing my face when everyone else is done and things are starting to happen that I'll miss if im eating. Venue people are not photographers and dont know what really is best, so ignore them if you can. (Just don't get yourself kicked out)