Ok, so it looks like there's a stat issue on at least the light sabers. It appears that light blue crystals are level 56 and the purple ones are only 48. Thus, giving Rep's a +10 crit versus Empire.

Not sure how many weapons this applies to, but I bet it's enough to warrant looking into it.

http://dulfyforce.files.wordpress.com/2012/02/empirerepubliccomparison.jpg