From your description I understand that the sound is fine at the church so long as the volume is low. In that case it would be helpful to know where you increase the volume. If you are increasing the gain within Hauptwerk then it is possible that you are overdriving some amp or speaker or that the audio is clipping, going into the red, within Hauptwerk.
Assuming that the HW audio indicator stays in the green zone it would then be helpful to try disabling one set of speakers at a time to see if the problem is in just one pair of audio outputs. It is likely that the dais (?) or Bose speakers aren't up to the task.
From the description it doesn't sound like the problem is related to the church acoustics though that was my first thought. Do the speakers sound good if they are closer to the organ? Again, I don't think this is the issue and suspect too large an audio signal out of HW or issues with the amp or one set of speakers.