Another swimmer on the forum!!! HOLLA! My crohnie is a competitive swimmer and there are a few others. She swims 2 hours a day 6 days a week. It has been great for her and we use her times as a barometer as to how she is feeling.
http://programs.rmei.com/CCFA139VL/start.html
Here is that webcast that I found extremely helpful when we were faced with the decision to add something to my daughter's Remicade treatment. Unfortunately, I poured over all the data and finally came to terms with adding Aza and the doc said Mtx. I wouldn't approve the Mtx because I hadn't yet done my exhaustive mommy research on it and asked about EN. Luckily he was very supportive of EEN (don't ask me why I had to be the one to bring it up as an option). So we all decided EEN for 6-8 weeks and if EN failed we would move to Mtx or Aza. EEN was just the boost the Remicade needed to get her into remission where she has stayed ever since. I wish your doc would give the Exclusive EN a chance. It might be just what he needs.
We only recently added Mtx to clear the Remicade induced psoriasis which is mucking up her blood work. Like I said before, the liver issues scare me way more than the lymphoma risk but at least we can test and respond so I accepted that risk.
Sounds like Aza isn't really working all that well for your son and that may be why the doc suggested Mtx.
I have to tell you while the biologics scared the begebees out of me when she was first put on them all meds on the table I would pick a biologic. Almost no side effects and while the risks are scary they are low. Compliance is assured (well until they start driving themselves to appointments) bloods at infusion so you get regular feedback with fewer pokes and more convenient.
Have you looked at LDN as an option? It is supposed to have the most minimal risks. Check out the treatment forum for some threads on it. Unfortunately though there are not a lot of ped GI's who are willing to try it but you owe it to yourself to check it out and ask at least.
I hope the presentation helps you. It doesn't include Mtx but like Clash said they are very similar in risk profile so.....
Good Luck with your decision!