I feel for you and can relate. My son has been 48" tall and about 48 lbs for about four years. The meds for this are scary. You have to trust your instincts. Insist the docs follow your son closely by doing and reviewing blood work often...no less often than every three months.
We have been "climbing the medication ladder" ourselves: Pentasa (oral), 6MP (oral), now Remicade (infusion). Each one of these is great, when it works. The problem is getting to the point that you know what will be effective for your son. Crohn's is a very personal disease. What works for one may or may not work for another.
Good luck to you both.
My mother has passed away from taking Metotrexate for 30 yrs. It eats your liver away.
I am not familiar with the injections, but I would assume it would be similar.
Good Luck with your son, I hope he feels better.