Coming up from the floor is not an option due to aesthetics......church feels it would interfere with worship.
Yeah. I've recorded in churches before and it's almost uncomfortable using a stand; it almost always feels out of place. I wouldn't do it as a long term solution unless it was the last resort.
We're moving off the board because it's a very "dry" signal coming out and requires the sound crew to maintain both the channel aux feeds to the recorder as well as the live sound. We felt a live stereo recording would be less maintenance and possibly provide a better sound adding the room acoustic etc. It will also capture the sound of the worshipers which we see as a bonus in this case.
I'm with Hyp; I'd pick up omni caps for the C4s (or the smaller AT mics he mentioned) and feed the mics into the sbd and route them to the aux outs only, then do a couple of test recordings with choirs or sermons to get an ambiance guide for how much signal to feed from the two mics in combination with the other sbd channels to get the proper mix. Only hitch will be calculating proper delay in milliseconds between the C4 pair and the other inputs/sounds. That would be optimum in my mind.
Baring that, I'd probably do what you're doing, but still use omnis. Just make sure you put the caps equally close to each of their respective stacks/PAs.