I have a very good health food store with a knowledgeable owner. If she suggests a certain root or herb, can I use it safely for Crohn's disease?

Avoid. My personal preference is to stay away from herbal remedies for a disease like crohn's. They don't work and can delay your getting proper treatment and place your life at risk.
Not recommended. As reputable & knowledgable about herbs as this store owner may appear to be, in all probability she doesn't know as much about crohn's as your physician. Some "herbal" or "natural" products have real potential to harm you. Short of weighing the purchased herb, she won't fully know the potency of active ingredient(s), unanticipated contaminants, risks of allergic reaction, bleeding & crohn's flares.