I was once a cathedral chorister (back in the late 60s) and there is (or should be) a natural balance between the organ and quire. Ours (at the time) was a damned good choir and we toured, sang at Windsor castle, etc., and recorded an album for Decca (now long deleted sadly - some lovely choral work on it). But anyway...
It was mostly done with a stereo pair of mics place appropriately. Sometimes, they'd have a mic for decani and another for cantoris mixed with the stereo pair but overall, it was a pretty simple, self-balancing recording.
Not quite the same but my daughter's involved in all sorts of youth orchestras as a violinist and I have made some reasonably decent recordings of their concerts with just a Tascam DR40 on my lap as I sit in the audience. If I could place that better (on a stand behind or in front of the conductor, perhaps), I am confident I could make decent recordings. Not Deutsche Grammophon perhaps but pretty reasonable, maybe/probably even releasable.
I fear you're worrying a bit too much about this but if you have genuine concerns, is there a way you could organise a quick run through with the choir and organist aforehand to practice getting some levels and mic placement, balance, etc.?
Website / Music Lab Machines / Blog