Are there ways for the immune system to be re-programmed?

Yes & no: In some ways, your immune system gets "reprogrammed" every time we encounter a new germ by "learning" how to combat it so that it is eliminated better the next time it is encountered. This memory feature is harder to reprogram. Some memory fades over time (hence the need for booster shots); o/w immunosuppresants are used to dampen an unwanted response (as in preventing transplant rejection).

Immune system: The only true way to re-program the immune system is with a bone marrow transplant that wipes out all the existing stem cells and then replaces them with donor stem cells.