Guess you have never played or seen anything Star-Wars-related. Consequences for alignment are fine, but these specific consequences don't make sense and they don't have any benefit to them. By the way, the Knights of the Old Republic games didn't have alignment restrictions on colour crystals.
Let's get a few things straight:
These restrictions have NOTHING TO DO with Jedi or Sith, they are alignment restrictions and affect characters of all classes (colour crystals are used in blasters too). Red, green, and blue are not associated with 'light' or 'dark side' by anybody (in fact most in the galaxy are probably unfamiliar with/don't believe in these concepts). Even if they were, this would not influence your ability to use certain materials in the construction of your weapons. Not all Jedi use blue or green, and not all Sith use red (in any time period, except sometimes when there have only been two remaining Sith). There are Jedi that use red lightsabers (like Adi Gallia) and there are Sith that use green and/or blue (like Exar Kun, inventor of the double-bladed lightsaber).
Here's a little Star Wars history lesson:
Originally, Jedi used naturally-formed lightsaber crystals of all colours freely, and so did the 'dark' Jedi who branched off, and then the original Sith (who kept their original lightsabers). When the Sith had need for new lightsaber crystals and they no longer had easy access to the crystal caves (which were frequented by Jedi), they started making synthetic crystals, most (but not all) of which were red. Even then, not all Sith used synth-crystals, and not all synth-crystals were red. Hundreds of years after the original Sith were disbanded and dead, Revan and Malak - inspired by old Sith holocrons - created a new and different 'Sith' organisation that was more political than just religious. They both started using red lightsabers probably in an effort to imitate the 'Sith look' that they saw in the holocrons, perhaps not even realising that the Sith were just using synth-crystals (though Revan used a violet one as well). The lightsaber-wielding followers of Revan and Malak followed suit. Following this, red lightsabers became associated with 'Sith', but it was certainly never a rule in any Sith organisation that you had to use a red-bladed lightsaber (in fact, they believed heavily in individualism and liked to customise their appearances to their personal preferences). Blue and green didn't become the dominant colours among Jedi until thousands of years after the events of The Old Republic. It was after the Battle of Ruusan, in which many crystal caves were destroyed and the Jedi's supply of natural crystals became mostly limited to green and blue (if I remember correctly). Even then, crystals of other colours could be found, and some Jedi used synth-crystals as well. The Empire in the original trilogy shot green plasma bolts, and the rebels and blasters in general were seen shooting red ones.
But as I said, the restrictions have nothing to do with Jedi/Sith or Republic/Empire, they are ALIGNMENT restrictions. Poorly thought-out, nonsensical alignment restrictions.