Hello! I have shodan (a 1st degree black belt) in judo and am also one short of that grade in kendo (traditional Japanese swordsmanship). I passed both of these grades with Crohn's (and before I started remicade).
However I have found doing martial arts with Crohn's tough. I have never been totally in remission, even during my first (and best) nine months of remicade. I have to deal with anemia as well, which made it hard to keep up at times in class. It was always frustrating putting in lots of extra training, but not being able to build that much stamina. I failed the black belt test for judo first time around too!
Dealing with extreme temperatures was also a challenge. Judo was always hot, while kendo could range from very hot to very cold. My gut never liked doing kendo in winter.
An understanding instructor helps, but it's your training partners that really matter. But another issue is how many people do you really want to tell about CD?! It can be hard to make excuses at a dojo! My judo instructor knew I had some thing going on health wise, but I always tended to play it down. I probably should have been more upfront about it!
It all depends on your own health situation, but martial arts are totally doable. As with any sport, you just have to take care of yourself. Go for it!