I'm not sure about Pilonidal Cists. Sounds like ingrown hairs are the main cause. So even if you treated the infection with the Beck Protocol you would have to do something about the cause of the problem.
Pilonidal Cyst Causes
Though there are several theories, most researchers believe that pilonidal cysts are caused by the penetration of loose hairs into the skin. In response to this ingrown hair, a local inflammatory reaction causes a cyst to form around the hair. Excessive pressure or repetitive trauma to the sacrococcygeal area are thought to predispose individuals to develop the cysts and/or irritate existing pilonidal cysts.
During World War II, more than 80,000 soldiers developed pilonidal cysts requiring hospitalization. Because so many of the afflicted servicemen rode in bumpy Jeeps for prolonged periods of time, it was termed "Jeep disease."