My point is that if you put the drummer far enough behind the organist and have the organist track the drummer by eye instead of by ear, the speed-of-sound-induced delay will match the organ's mechanically-induced delay and everything will sound right.

Another option would be to place the organist next to the drummer, but keep the organ itself far enough in front of the drummer such that by the time the sound comes out it's in time with the drummer. I don't know if there are any organs that work this way, though (I'd imagine it'd have to be either mechanically complex or electronically controlled; the latter, though, gives an option for a synthesized "monitor" that the organist can hear, which should hopefully make the delayed sound of the actual organ less of a mindscrew).

This all assumes you have a large enough stage to be able to pull this off, and (in the case of fixed organs) have actually built the organ such that the sound does emerge from in front of the drums.