I remember that too, I think it was from the X wing series, or maybe I, Jedi. Corran had to get a lightsaber fast, so he synthesized a red crystal. However, in the more recent books, we've discovered that when jedi and sith tune their crystals they change colors. I forget the name of the book, but one jedi took a crude red crystal made by a crazy clone and retuned it to yellow. I didn't get the impression that the jedi had a lot of say in the final color as he was surprised that it came out yellow.
So based on that, I think the colors should either change autmatically to reflect your alignment, or be selected automatically whenever you get a new saber.