Actually, Ironman, high rep and/or heavy squatting motions can aggravate a condition that involves frequent, uncomfortable bowel movements. This is due to one of the physiological benefits of squatting - more frequent bowel movements. SO if someone's condition is aggravated by frequent bowel movements, or someone is interested in reducing the number of bowel movements he/she has, squatting motions might be an issue, especially under high-rep/heavy resistance conditions.
Some interesting articles here
Having said that, i am not an expert on crohn's, but this might be of consideration.
Now, on a different note, if the program Fish is looking for is only cardio - i agree, there shouldn't be an issue.
Perhaps, FIsh, you could give a little more info regarding current situation and targets/goals and someone here can help you out.