I think I would have said:

"I am doing pretty well - there are good days and bad days". Then something along the lines of "not everyone with MS is outwardly disabled and the strangest part of this disease is that so many of the symptoms we deal with are invisible to outsiders. I am happy that my disease is not obvious to you."

Then, close with something like "I really don't like discussing this too much, but if you are really interested in knowing more about MS, the NMSS website has some great info."

That would be if I was behaving myself. If I was really being pissy, I might do what Shelley suggested!

My priest said he had an eye opening experience when he told a parishioner who has an autoimmune disease that he "looked so good" and the guy shot back "well, I wish I felt as good as I look then". He said that made him more sensitive to those of us who have invisible disabilities.