With the removal of alignment restrictions during the early months of 2012, color crystals in Star Wars: The Old Republic have pretty much lost any "traditional" meaning they may have once had. In the good old days, the bad guys had red and the good guys had blue or green, just like in the movies. There have always been oddball colors - orange, yellow, purple, and the black-core variants of all the other colors - but the three primary colors of light remain the Force-user standards. Jedi use blue and green, Sith use red.
Read more about the historical precedence of SWTOR's color crystal variety with Color Crystals: What's In Your Saber?