This may be showing my lack of experience or knowledge, but do you really think you're going to need a flash? I guess what I'm saying is that I would first try to get by on bumping up your ISO while shooting with a large aperture. And I agree with zona that you should take along your 50mm f/1.8 as well. I would think increasing your ISO (800 - 1000 perhaps?) and shooting at f/1.8 - f/2.8 would give you the shutter speeds you can work with. The 5D Mark II is more than capable of handling the higher ISO setting.
Of course, I would take along the flash just in case. Is there any chance you can get a preview of what you'll be working with ahead of time so you can get an idea of the lighting? If you're forced to use your flash, I would shoot full manual. Like you said, if you shoot in Av, most likely, your camera will want to use some pretty slow shutter speeds. I recently did some photos at a wedding (I wasn't "the" photographer), and I was shooting at ISO 400, f/2.0, and around 1/100s. I can't remember exactly, but I think my flash was set to E-TTL. And since your flash is (presumably) going to be shoe-mounted, you're going to want to bounce the light, so take note of the walls/ceiling around you. That's where getting a preview of the location would help, or at the very least, show up early to give yourself enough time to check out the location and maybe take a few test shots.
Hope this helps, and I hope the photos work out.
