I have a 10 yr. old girl who was diagnosed with this last year at age 9. First let me say, I'm so sorry you and your child are going through this. It's truly scary when you don't know what to do next, or how to help your innocent child. I've felt that same way.
As for what to do, I would highly highly agree with those who have recommended that you read "Breaking the Vicious Cycle" by Elaine Gottschall. This book may be a strong first step toward healing and understanding. In our case, my daughter refuses to eat the recommended foods and so we went the medicine route. She is doing much much better a year later and has gone back to life as normal (most of the time), except for the fact that she now has daily meds to take. We did start her with prednisone, which had her gain about 20 lbs. and blow up like a balloon, but most of the swelling and about 10 lbs of the gained weight dropped off within months of stopping the medication. Personally, I'm still hoping that when she matures she'll be more willing to try the Specific Carbohydrate Diet discussed in the book as I do believe it would promote better health and less Crohn's complications. Perhaps since your child is only 3, you'll be able to manage her diet and change it quite easily.
Thank goodness you finally found a doctor to recognize what is happening to your poor baby!
BSMOM - Oh, please don't cry! Stay strong and do what needs to be done to help your daughter feel better. Things WILL get better and she can lead a normal productive life with Crohn's. As my daughter's doctor says to us regularly (which always makes us feel better)... "Crohn's shouldn't control you or your life. We will help your daughter manage this disease so that she can live a normal happy life like everyone else." So far so good for us. Stay positive, it helps!
PS. Others here have found great help and healing by doing an elemental (liquid) diet. Try looking into an option called EO28 Splash for children. Some put their kids strictly on this liquid diet until remission of symptoms sets in...then reintroduce foods slowly. Others use it as a supplement to food. You will find it if you Google it. Good luck! (My daughter drinks ENSURE regularly to keep weight on and for nutritional purposes...but only like a bottle to 1/2 bottle of it per day.)