I think if you really have a strong desire and a passion to enjoy and practice organ music, you can remember that organ practice is primarily a mental activity which of course involves the entire body.
Although you might not be able to move your legs, you could still practice manual pieces on the organ or on any keyboard instrument, such as a piano. There is such a vast amount of unexplored repertoire for hands only which you could take advantage of.
You can also practice on the instrument without a score. Here you simply memorize your piece or pieces and play them on the piano or a similar keyboard instrument. You can do it without using your feet while sitting in a wheelchair.
Another way to practice is on the table with the score. You can sit in a wheelchair and pretend you are playing the keyboard. Move your fingers on the table as you would on the manual.
Also try to practice with the score sitting anywhere you want, not necessarilly at the table. You can keep your hands on your lap. Your fingers could move in one place.
The last method would be to practice without a score and without an instrument. Memorize your piece and play it on your lap. This is a very powerful way to increase your mental capabilities because you will have to learn to hear the music in your head.
Apply any or all of the above tips in your practice if you are in a situation where you have to sit in wheelchair. Your medical condition should not limit your passion and dream in organ playing.
Do you use any other methods of practice which would be helpful for people with various disabilities? If so, share your thoughts in comments.