Exercising, while being a rigorous activity, actually helps reduce stress and improve digestion for most people. As long as you're not in flare-up, I don't think it should be a problem. Basically: don't do anything you're uncomfortable with.
I also found an article about it
here, if you're interested. It also has tips at the bottom and the next page on exercises that might be easier on your body if you have Crohn's.