I would most definitely ask your GI before trying EEN. Your GI needs to be kept in the loop, even when you try things like supplements or formula. EEN is great for inducing remission but I think you need to change his maintenance med, just as others said above.
Methotrexate (MTX) is NOT considered "chemo" in the doses used for IBD. Those are teeny tiny doses compared to what is used for cancer. I know a child with leukemia (who doesn't have IBD) who was given over 1000 mg of MTX as treatment of leukemia. At most, kids with IBD are given 25 mg. Often lower doses are used. My older daughter takes 15 mg for arthritis.
She has has mild fatigue the day after the MTX injection and some nausea, but usually Zofran takes care of it.
The other option would be biologics. Biologics are the ones I'm guessing you are scared of. We all were scared of them and we all worried and agonized about giving them to our kids. I spent many sleepless nights worrying about if I was doing the right thing. Our pediatric rheumatologist at the time told me that once you try biologics, you never look back.
I can honestly say we have NEVER regretted using them, not for a moment. They gave both my girls their lives back. My girls had been in pain, not sleeping and miserable before we tried them. After the biologics kicked in (we started with Humira for both my daughters), they were back to their happy selves.
My only regret is not putting them on biologics sooner. Both my girls have some permanent joint damage because we didn't start earlier. I wish we had treated them more aggressively.
So once my younger daughter was diagnosed with IBD in addition to the arthritis, we acted quickly. She was already on MTX, but we stopped the biologic she was on (Enbrel, which treats arthritis but not IBD, which is why the IBD showed up) and put her on Remicade.
8 months after started Remicade, we repeated scopes. Her scopes looked SO much better than at diagnosis!! It was really amazing - ALL the ulcers in her colon had healed. Her colon looked so good that the GI said it looked like she didn't have Crohn's! She still had slight inflammation in her terminal ileum, but even that was much improved.
Since we treated her IBD aggressively, her IBD has stayed mild and she does not have permanent damage.
At some point, the disease becomes scarier than the medications. IBD medications may potentially cause side effects. But untreated Crohn's WILL cause complications - strictures, which can lead to obstructions, perforations and sepsis, abscesses, fistuale and growth delay.
My daughter also has adrenal insufficiency due to steroid use. Her adrenal glands essentially just shut down because she has been on and off steroids for her arthritis for years. Her endocrinologist will now allow steroids to prevent joint damage but we REALLY have to keep her off them as much as possible.
Her adrenal glands had pretty much stopped making cortisol and ACTH. Her cortisol levels were undetectable when we tested them and since she was having symptoms, we had to rush her to the ER to get hydrocortisone. Her endocrinologist was worried she was heading into an adrenal crisis and she was (and those can be fatal).
It took months of daily hydrocortisone before her adrenal glands "woke up" and started producing cortisol again.
Now she only takes cortisol when her body is under physical stress - if she's had a lot of diarrhea and is dehydrated, if she is sick with a fever, if she's in a lot of pain, if she's having anesthesia etc.
You need to see an endocrinologist for adrenal insufficiency because it can be very serious.