I watched that episode of The Clone wars after seeing this video yesterday, and all of the crystals the younglings harvested were a pale, white-ish, watery blue color. Then, after making their lightsabers in the next episode, two of the blades were green.
I also remember having read an EU novel called "Riptide" where Jaden Korr (from the Jedi Knight; Jedi academy games) took a lightsaber from a deranged clone of a New Jedi Order Jedi knight and remade the red crystal by removing the dark taint from it by focusing his will and nature of the Force into the crystal, essentially cleansing it and restoring it to a natural, white colored state, and finally turning the crystal yellow. I skimmed though it again, and this takes place on pages 60-63 of that novel, and even though it is considered to be a Legend series book, now has some basis in canon.