It would be easy to reply w/ "You do the crime, you have to pay the time".....because I have worked in the justice center all my life, but not sure if that is appropriate here. Without knowing the specifics, where I would start at is asking ,does he have a lawyer? I'm not sure if his CF disablity excuses him from jail or he is being disriminated against because they sound like they are provding some medical care w/ anitbiotics, just not enough.
When he was sentenced did the judge know of him medical condition, and if he currently has a CF doc, prehaps he could write to the judge and asked for him to be considered for early release to possibly be admitted into the hospital or home incarceration.
Wish I had better answers but hoped this helped a little. Don't give up, it sounds like your son needs you.