DS22 (the son I rarely mention [:P]) was tested to have a latent version of a potentially serious/fatal disease. It was the kind of thing where 9 times out of 10, he would never develop the actual disease, but in the event that he did, he would be quite ill and loaded down on drugs. Anyway, to get rid of the Latent bacteria, he was supposed to take a medication for 9 months. This medication left a risk for liver problems, so he had to get checked out for that very frequently. He was *extremely* reluctant to take the medication, though he eventually did, and he turned out fine. He is still a wreck about medications, though, I don't think his "success" made anything better as far as not being nervous in the future goes. I also hope he doesn't find out about the recent linking of Accutane to abdominal illness, I don't know how I ever convinced him of taking that in the first place, I guess he knew his acne was incredibly severe, though. The same son also suffered from migraines and didn't get treatment, they eventually stopped happening as frequently around when he turned 20. I imagine your son's situation is worse, though.

I know that doesn't help you too much, but I do find it interesting that our family went through a similar situation. I don't think you should try to force him into taking it, but getting statistics from a doctor on the prevalence of the side effects would definitely calm 2 of my 3 medication-scared children, and if the risk is too high for comfort, like others said, maybe you can try to find an alternative medicine.
Anyway, good luck with everything, I know how difficult it can be to see your children suffering but afraid of the only thing that could make it better.