Why did they say you shouldn't take iron supplements? I understand that many GIs are afraid to prescribe oral supplements because they MIGHT irritate the intestinal tract. However, no studies have proven that they make Crohn's worse. I emailed the researcher of a study trying to prove oral iron could make Crohn's worse, but she replied that the results were still being analyzed.
Low iron affects your immune system and even affects your learning and memory skills. Some docs wait until you have anemia to treat low iron. This is a mistake, because by the time you are anemic, harm has already been done.
If your doc is doing just a knee-jerk, "I'm afraid to prescribe iron because it might make Crohn's worse," response, then it might not be a good enough reason to deprive you of the benefits of oral iron supplementation.
My daughter's health has never been better, since she has been taking iron supplements - Solgar's Gentle Iron, 25 mg daily with OJ. (Don't take with food or other vitamins, and don't take within two hours of other vitamins, meds, or food because they tend to interfere with iron absorption.)