good.jew — It does not seem that the OP’s main concern with regard to negiah was the handshaking issue. (These are classmates — presumably the handshaking dilemma has passed for the most part!) It seems she is more concerned about working on group projects, etc.. where other situations of negiah arise.
I do agree that there is no reason whatsoever to lie, and it is highly inappropriate (and probably against Halacha) to do so. As other posters said, there is no reason why one cannot politely and matter of factly explain this issue the same way one would explain not eating non-kosher refreshments. The worst case scenario is a few strange looks, and some classmates who think you’re a bit strange (which may not be such a bad thing. . . )