Autoimmune conditions result from an imbalance that is too yang, too fire-based. Although some deny it, reiki seems to be a yang sort of energy. So IMHO, sending lots of reiki into someone who's going through an autoimmune flare-up runs the risk of exacerbating the imbalance.
Re. treatment, sending yin energy (flows from the ground up, water-based, and relatively cooling) has alleviated the flare-ups. Especially if yin energy is moved into the recipient's bone marrow and the area around the heart and thymus gland. It's helped w/ conditions like rheumatoid arthritis, fibromyalgia, and autoimmune hypothyroiditis.
Bruce