Hi,
I don't think there's any particular god or goddess or other "guardian" of crystals in Greek myths, but I remember a Russian fairytale about the "Malachite Goddess" whose name was, sometimes, "Sinyoushka".
M. Bazhov wrote an entire book of interlinked fairy tales from the Ural Mountains, based on real tales miners in the Urals used to tell.
The Malachite Goddess appeared as a young girl, or an old witch, or an enchanting sorceress depending on who it was that met her, a man usually, and how he behaved.
She could be playful or bestow gifts (like having a man who had fallen in love with her meet and marry a girl who looked exactly like herself, so the man and girl lived happily ever after) but could be very dangerous too.
She wasn't only a guardian of malachite but a protector of the earth, of rocks, and crystals and gemstones. She also had an affinity with the moon and she usually appeared at night dressed in greenish blue.
I've read she was based on a much older deity, protector of the Urals.
"Sinyoushka's Well" was the only fairytale I had read translated in Greek when I was a kid and loved it because it was so magical and mysterious.
There's an English edition available with all the tales "The Malachite Casket/Tales from the Urals" (which I bought and read in one sitting a few years ago) but maybe you'd also like to check the links below as they have some info, and more links, about the Lore of gemstones and crystals.
http://www.mythinglinks.org/ct~landscape~minerals~malachite.html
http://www.endicott-studio.com/rdrm/rrGemstones.html
http://www.sunbirds.com/lacquer/readings/1138 (Outline of Sinyoushka's Well.)
Hope this helps.