First of all, :grouphug:
I have a family member with Crohn's and it has been really tough, but there is help out there. You are absolutely right that diet plays a key role in dealing with this.
I recommend the following books: Breaking the Vicious Cycle and Gut and Psychology Syndrome. Don't let the title of the latter one throw you. It is very good information on diet relating to any inflammatory or auto-immune condition. It's a long read, but tons of great info in there.
As a parent, the meds would be a very tough call. I understand where the Dr. is coming from. Inflammatory conditions can be worse it kids due to the constant changing nature of the body. Those meds are life savers for some, but they do come with side effects. Do as much research as you can before you make a decision. Although, if meds are needed, don't be afraid to reach out the the Dr. for help.
If it were me, I think I would try the diet first. And I mean go at it full force. Read all the books, medical studies, and other info available. Then buy whatever kitchen supplies you need to get started. For example - you might need a dehydrator, crock pot, pickl-it jars, or juicer. It will take planning, time, and work.....but I don't think you'll really be able to tell if diet can help unless you do it to the full extent.
Disclaimer: the advice is intended as opinion only and not professional medical advice ;)