I would be shocked and disappointed if that was the case. I am currently in a similar boat. Just found out I have Crohn's, and as a military pilot you're pretty much screwed. The big issue is, even if you're stable you can't fly as Pilot in Command.
Anyway, please let me know if anyone has any specific advice on the CAA's stance on Crohn's. I am currently taking PENTASA only to control the condition and have no side effects.