It may be worth a shot to discuss whatever issues you have with your school. However, from my experience, it's a hard thing to get past. Clinical sites require employees, interns, volunteers, etc to get their flu shots both for their safety and the patients. If you're going to be working with immuno-compromised patients, it's very important that you aren't going to be infecting them with the flu during your time working there. All of my clinical sites have required me to submit written proof that I've received my flu shot for the year before allowing me to work.
My personal opinion? If you don't want to get vaccinated, don't. But you need to sign an agreement that if you contract one the these diseases that could have been prevented by vaccination, we get to lock you away in an isolation chamber until said disease takes its course.