Actually if it's anything like MS, I could see how the stress of airline operations could aggravate the condition. Cyrcadian disruptions, chemical exposure, constant immune challenges from diseased pax, sun exposure, etc. I would be leery about commercial flying unless you are certain that you are not at risk for a recurrence. Recreational flying would involve much less stress.
For FAA medical purposes, it does not matter whether your goal is regional turboprop FO or major airline wide-body captain...airlines will require a First Class medical in order to get hired and the FAA standards will be the same for any pilot. However if you end up with a limited-duration (waiver) first class I suspect it would be easier to get hired at a regional vice a major.
I would spend some money on a medical consultant BEFORE you apply for an FAA medical.