My thinking is, given that you are going to have to do it no matter what, or whatever you say, to be as prepared as possible. But you already know that. So working down the risk list...
a) Beg, borrow or rent a second compatible body. We're talking camera body here, although photographer body is probably not a bad idea either.
b) All batteries are programmed to die just when you need them. Have seconds and thirds of all batteries you need. Charged. And bring the chargers.
c) If that church has windows, you can bet that the darkest cloud in the past twenty years will park itself over the church during the ceremony. So... you'll need flash. You have that. but you may also need to work with whaever ambient light they have, and tha may mean you should thinks of color gels for the flash to get the same white-balance.
d) Since flash is important, you can expect it to fail. Can you get/rent/borrow another flash?
e) Visit the locations and try to shoot as much as possible in those locations to get a feel for how the light bounces, where the dark sinkholes are (those parts of the room that ALWAYS are dark no matter how much light you shine on them), and where the glare lights are situated (you know, those lights that always seem to shine directly into your lens from vantage points that are key for you to use).
f) Photographer hat. That's the one you put on to let people know you're the OFFICIAL PHOTOGRAPHER, and not just another getting-happy family member.
g) It's family, so "contracts" may or may not apply, but it is probably a good idea to write down what your and their expectations are, and to have them say that they agree. At least, later, when the inevitable arguements about who was supposed to do what happen, you've got something to back up your version of events.
Oh, and find a four-leaf clover. I heard that they are supposed to be good luck.