Oh dear, crohns in a baby is outch.
Please, google pecanbread and read your way through the outlines of the special carbohydrate diet.
It was developed to help a child with crohns, it is easy and gentle on the gut, it changes the probiotic flora, reduces inflammation and nourishes the child on the long run. It also helps children and grown ups with autism, IBS, celiac, CFS and other problems.
Good luck!
The first link talks about some causes of chronic diarrhea (long-lasting) in children, so could be something on that webpage will strike a cord with you. The second link is one of many with information about the drug they're using. Now, as relates to that drug, one of the causes of chronic diarrhea in kids is a weak immune system. So, I hope these links will help you a little.
http://advancedpatienteducation.com/Diarrhea__Children_.html
http://en.wikipedia.org/wiki/Mercaptopurine