I have not been here in a long, long time....I had a 4+ years remission on Imuran, but my Crohn's flared-up back in November (and is still an issue).
In my experience, you're better off treating the disease and finding a good maintenance med. Your son has inflammation, yet is relatively "healthy" -- that was me on Imuran (I was underdosed). So, in those 4 years of symptom-free "health," I developed a stricture and this current flare is the worst one I've ever had...I've been on pred for over 5 months, and just cannot get off of it (personally, while pred brings fast results, I really hate it). I recently started Humira (which used to really scare me, but I'll do anything to get back into remission).
Personally, I'd rather take the 6mp than the flagyl -- the flagyl can really mess with the natural flora in the gut, and isn't really going to quell the immune response causing the inflammation (I will admit that I have a prejudice against the antibiotics -- had bad reactions to all of them). Pentasa and the like can work really well for some people, but they don't have a great track record for keeping people in remission.
In my nearly 5 years on Imuran, I can't say that I've been more prone to catching colds/flu (I get a yearly flu shot). If I do catch a cold, it takes me maybe a day or two longer to get over it. I work at a hospital, and I haven't caught anything here yet (I wash my hands a lot and keep my hands off my face). They'll be monitoring your son regularly if he goes on 6mp, and in my experience, my white cell count never dropped out of the normal range (though it tended to hover closer to the bottom of the range).
Good luck, and good health to your son.
Diagnosed with Crohn's in April 2003 (first symptoms in 2001).
Current Medications: Imuran 125mg/day, Humira, Pred 2.5mg/day, Cortifoam, Phenergan as needed for nausea (have previously taken Asacol, Entocort, Flagyl, and Cipro)
Dietary Supplements: Flax seed oil, Folic Acid, B12, Culturelle