Thankfully, I only ever had joint pain when I was tapering off of prednisone.
How much of the joint pain is due to having colitis and how much is due to having taken steroids? It's hard to know, because the worse the disease, the greater the likelihood of having taken steroids.
Figuring out how to reduce a flare or get into remission is a trial and error experience. Don't expect your GI to have all the answers. He was trained in making diagnoses, prescribing medications, and surgically removing the colon. He was not trained in alternative treatments. That's why they are called alternative treatments.
What works for me: Fecal transplantation, Probiotics, Anti-inflammatory foods, No HFCS, No crystalline fructose, No foods high in fructose, No artificial sweeteners, No pro-inflammatory foods when flaring, Vitamins, Lexapro (for stress).