The thing is, as we saw in Rebels & TCW, kyber crystals are naturally clear. The book even states that they can be forcably extracted by unnatural means, which is akin to what the Sith do so presumably "mining" them in the traditional sense would also turn them red. That they're already green suggests that a Jedi or other lightsider had a hand in it's initial purpose.
This seems to agree with the suggestion that part of the plot of Rogue One will involve such a one on Jedah, which is supposedly an (possibly *the*) ancient home of the Jedi. An ancient Jedi artifact like a large holocron secreted away in some hidden chamber is certainly within the realms of possibility.