It may be a stretch for it to exactly coincide with lore, but i think its a relatively small one. You can easily shoot off 100+ things that are much worse.
I would have previously agreed with the color confusing people, but i remember hearing that they are allowing color crystals for sabers to basically be free range from jedi to sith, light to dark.
It really comes down to color crystals being such a big thing for saber users. Bioware seems like they are going to put some work into getting rares ones. And then like michaelra said above, as a sniper i don't even pay attention to my color crystal.