My daughter had been taking melatonin for several years before her diagnosis. She has always been an anxious kid, and melatonin really helped her sleep. We asked her GI about it after diagnosis, and she said it was OK to keep taking it. I decided to take her off it though, since I had read that it could enhance the immune system, which seemed like it could counteract the immunosuppressant drugs she was taking.
After about 6 months off it, she was having a lot of trouble sleeping, so we asked her GI about it again, and she again OK'd it. So she's taking 1 mg at night again, seemingly without any issues. Like anything, I think its a matter of balancing benefits and risks.