To echo other replies, 50mg of Imuran is a really low dose. There is a blood test available to show whether or not you are in the therapeutic range for Imuran to work (it's from Prometheus labs, but it's pretty expensive -- I couldn't have afforded it if I weren't insured). I had been on 100mg for years, slightly underdosed according to weight calculations. My new gastro ran the test, and sure enough, I was underdosed (I'm now on 125mg).
Entocort never did all that much for me, but I would be a little leery of taking steroids long-term, even if their systemic absorption is supposed to be minimal. For long-term maintenance, I'd go with the Imuran. As someone else suggested, you could do both -- go on the entocort and raise your imuran dose...once you're stable, taper off the entocort and stay on the Imuran. Honestly, for me, Imuran has had the fewest side effects of any med I've taken (and I've been on a lot of them).
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, Glucosamine/Chondroitin, Calcium +D