Well put, Archie. A couple of thoughts:
1. From experience, Catholic churches always have policies like this. Generally, they view anything outside the liturgical ritual an unwanted distraction. However, not all priests agree -- you may have a presiding priest who doesn't give a damn what you do. Last time I did pictures in a Catholic church I talked with the priest beforehand and all he had to say was "Make sure you get my good side."
2. I see two choices. First, either make it explicit in the contract and make sure bride (and whoever is paying the bills) understands they may not get what they want because of this policy. Then do the best you can given the location. Second choice, once the ceremony starts, do whatever you need to do. They're not going to interrupt things and tell you to sit down. Be reasonable in your movements, but be where you need to be. In the unlikely event the priest gives you hell afterward, tell him you'll see him in Confession! I strongly believe in the adage, "Asking forgiveness is easier than seeking permission."
3. I immediately thought of the remote cameras idea. That may be a good alternative, especially if you can get something reasonably close and WA.
4. Given the church itself, it may be a great place for formals. You'll need to have a good lighting setup ready to go. Second shooter or assistant a must.
5. Just for background, the Catholics have been at war with funeral directors over this sort of thing for a while now. The Church feels the funeral directors are trying to take over the funeral mass. The funeral directors don't like being told they can't do what they believe they need to do. It's gotten quite unpleasant in some places. Perhaps this is bleeding over (so to speak) into the weddings realm.
Two things: 1. Discuss location limitations with the bride and make sure you have this in your contract (the Clients confirm they are aware of location limitations for photography). Clients need to have reasonable expectations. The location is their choice and they need to discuss this stuff with coordinators, priests, etc. They can expect certain shots from the back but they should not be expecting say low right angle shots from the first row, or side shots, etc. These are the limitations of the location which they picked, so they need to have a good understanding of this stuff before the wedding day.
2. Scout the location and have a chat with the priest. Speculating regarding lenses before that is really pointless.
Also, when i work with limited movement situations, I do bring primes but having zooms is a must.
30 minutes for formals is not enough. By the time everyone gets out of the church, all hugs and kisses, etc, etc and you will have 15 minutes left. Are you doing formals right next to the church? Are you doing formals of the wedding party or family shots? Family shots take longer. Well posed formals take longer. What if the weather is bad and you need to drive to an indoor location? Talk to the priest and maybe he will allow posed wedding party shots inside the church with the flash after the ceremony is done. More importantly - discuss this with the bride so she has a clue of the impact of time limitations.
Planning is the key, especially if you are just starting with weddings.