I have done a couple weddings and all of them had the situation you are referring to. Lightroom 4 helps with it's ability to use the adjustment brush to fix lighting, but it takes a lot of work and still doesn't turn out perfect. Most weddings don't allow flash during the ceremony, so you are stuck with the lighting you have. Shoot in RAW. I have always had someone stand directly where the bride and groom will be prior to the wedding starting with the same light it will have and have them hold a gray card. You could stand there and do the gray card trick yourself also. That way you'll at least have the light the temp you want. (just don't forget to set it back later if you choose this path). The other option is black and white. Here are a couple examples of my black and white stuff. You can see the light shining from up above. It was nasty light. I shot this with a 7D, 70-200 f/4 IS at f/4 and either ISO 1600 or 3200. Can't remember specifics since it was a couple years back. Processed in LR3 and CS5.

Its not the best solution, but the one I chose. I don't shoot weddings for a living and hardly do much photography anymore. Maybe someone else who shoots weddings for a living can give you a better pointer.