Joint pain is not usually a major issue for me, but I do get minor joint pain (and stiffness) with flares. I just started aza/Imuran about 5 weeks ago, so other people's experiences may be more informative than mine. But I am definitely feeling better overall (joints included) than before I started it. I completely understand your hesitancy about going on an immunosuppresant and I put it off for basically as long as I could. However, I am very glad that I decided to try it, because it seems to be working well for me with very limited side effects, and I actually wish I hadn't put it off for so long. I was very worried about the potential side effects (particularly long-term) of trying immunosuppression, but I eventually realized that the risk would be worth it to me if it meant that I would be able get my Crohn's symptoms under control enough to be able to live a relatively normal, happy life. I'm already noticing a big improvement in my quality of life and my GI just told me she thinks I'm on my way to remission.
I'm not saying these drugs (Imuran/6mp) are for everyone or that you shouldn't try other things before resorting to them. I just wanted to give you my experience and suggest that if the joint pain is having a major impact on your quality of life, you weigh the potential risks/side effects against the potential benefits of the medication, rather than thinking of it as something you'll try to avoid for as long as you can. Also, essentially all of the side effects from short-term immunosuppression are reversible, so there's little risk in trying Imuran/6MP for several months or so (assuming your doctor is getting frequent blood tests to monitor for potential problems) and seeing how you respond. You may already know this, but Imuran is actually approved on-label to treat rheumatoid arthritis, so it could be a good option for you in the future.
I'd agree that if you haven't already, seeing a rheumatologist could be helpful. If your GI deals with a lot of IBD patients, she/he might be able to recommend a good one who has experience dealing w/ Crohn's patients.
21 years old, diagnosed with CD at age 18,
First major flare since diagnosis started in Nov. 08. Still recovering and mostly stable, but having trouble tapering Pred.
Prednisone 12.5 mg, Azathioprine 75 mg (just started 5/03, but think it may be starting to kick in), Asacol, and Rowasa
Plus Vancomycin and Florastor for a recurring case of c diff.