Judy,
Actually, the more a pipe organ is played, the better it stays in tune and remains in better mechanical condition. Were any reasons given to you for their change in policy?
Not knowing the physical layout of your church campus, but if the parish offices are attached to the church where they can hear your practicing, maybe that is disturbing them, especially if you are there every weekday for endless hours. I have this similar situation - I can't practice much during the daytime hours ... if I do, I have to limit my registrations to 8' & 4' flutes and no 16' in the pedal. The office staff has to wear earplugs when the organ tuner comes ... lol. Maybe this is the reason for them not wanting you to practice for hours on end many days of the week?
You mention other churches with Hammond like instruments. Are any of those full size consoles with 32 note pedalboards and 61 note manuals? If they are, that might work - granted not the same sound, but as the late Virgil Fox once told me "it's not the sound that matters - it is the fingering and pedaling practice ... the sound follows what the fingers and feet are doing, so the real importance is what you practice, not on "what" you practice on."
I frequently practice organ pieces on my piano at home ... sans the pedal of course ... but once the manual parts are learned, the footwork comes along nicely. It's amazing how much better my articulation is on the organ after practicing on the piano ... it really works.
You might also check with a local music store - maybe they would let you practice a few hours a week ... I did this in my early student years before my folks bought me a full sized organ to practice on at home.
There is always a solution for every problem - sometimes the search takes longer than what we think it should.