I think Amonite may be onto something, Torq: the mosaic tile may eliminate the "bathroom" feel by taking care of what I think is the true issue: the squares are far too large for the scale of the monastery. I would at least halve the size (if not more!).
Also, would the builders spend the time putting patterns below the pews? Maybe instead place an inset tile border along the edges of the pew areas? (Actually a true Orthodox monastery would have no pews but (perhaps) along the walls--but I realize we're fictionalizing here.)
Two other suggestions: 1) the stained glass windows are in deep perspective, but the walls are not; thus the illusion is broken. I'd make the walls also deep 3D or eliminate the perspective on the windows. 2) the dead body is cheesy & cartoony IMO; I'd get rid of it or make it more lifelike.
Just some ideas to help; overall looking great. I absolutely love the mood you've created! Keep it up!