I have Crohn's also. I understand when someone suggests trying to use the bathroom before getting in line and I do but that does not help the mad dash that us Crohn's warriors all take too often. My great fear is for it to happen while on a ride!
I suggest midday breaks at the hotel to nap or even relax in a pool chair. Resting relives some fatigue & lowers stress (one of our triggers).
Learn where the restrooms are. Something I am sure you already do most places you frequent. We both ran through MK last trip searching for one when I got confused in my panic to find one. I studied my maps that night! My DH laughs that I now have restroom radar
Take individual packages of wet toilet paper wipes.
What may help you in those bathroom lines is a restroom access card. Not found through Disney but found online and you can print it out. Looks more official, which helps those people become a bit more understanding. You can find them to print free here chttp://myibd.org/RestroomMedAlert/index.phpan
Hope I helped some. Have a great trip!