You'll need to talk to your instructor(s) but I have seen some accommodations made. I'm not sure how much lift you need, but if you can fit some kind of orthotic into a cotton bottomed tabi, that would probably be the most appropriate solution. I've seen some people who had a similar issue who wore "dojo" shoes that were just running shoes that they never wore anywhere but on the mat. Frankly, I dislike that solution because it's too easy to accidentally injure your training partners and is almost impossible not to damage the training surface. A cotton bottom tabi would look better, not damage the floor and be safer for your partners.
I would also tell you that sometimes those diagnoses are incorrect. I had a pinched nerve in my back that was diagnosed by several PTs and an MD as partially due to different leg lengths. This was causing severe debilitating pain for months and months. I saw a bodyworker who specialized in a similar method to Rolfing and he said they were flat out wrong and that I had a muscular imbalance in quads/hamstrings that was pulling one side of my pelvis down much more than the other side. This was putting almost a 1" twist in my hips. Since the doctors were measuring the length of my legs from the top of my pelvic bone (in the front) but not looking at the overall shape of the hips, they were not correct in their assessment. I saw him for two sessions and combined that with two visits to a very good acupuncturist (to help release the muscles that were causing the imbalance) and my pain went away and has not returned. I don't want to sound like I'm second guessing your doctors, but you might look into some other options if you haven't already.
+1 from me on the leg-length thing. If I would have gone ahead with the orthotics it would have made the problem worse. After a very simple treatment by my shiatsu practitioner, I was pain-free, my back problems went away, and no doctor has ever measured different leg lengths since.
Also: back pain is horrible.