Interesting post! There is actually a new therapy in development that can specifically target proteins for activation and then destruction in the proteasome. These things are called PROTACs and I think some Princeton scientists came up with it, might be interesting for you!
As for prions, they really do mess up the germs theory of disease because they can cause other proteins to misfold. I cannot remember exactly how, but they do evade the proteasome system and do not cause any symptoms for years. They build up before reaching a critical amount, when the disease breaks out. It is pretty funny though, that while cause a disease (Prp Sc) the Prp wildtype seems to be serving a purpose. Anyways, cool post. Cheers!