I am not sure but somebody mentioned 15 or 16. I got 4 from quest in High hills found 2 in a cave with books and 2 or 3 in grave robbers cave. You can also get 2 from Khan but it will cost you dearly.
Remember, you have to give 2 gems to philosopher in exchange for 2 skill points.
You’ll definitely not get back any resources from disenchantments and charms are permanent
I bought 2 from a merchant in Broken Valley village, get 1 from waking up the 3 sleeping dude in broken valley, 4 from high hills quest and another 1 from mind reading the goblin under the ancient tree.
Bout the grave robber cave you mentioned, is it the bout the quest grave robber where you collect 2 quest item from dead body and meet another 2 outside the cave, after going in and found that its a stupid joke by bellegar? I dont think I get any malachite gems through this quest.
Update: Just obtain 1 more from depleted ore mine where the 3 books is locate. Seems like those malachite ore vein will randomly give malachite gems. Now got total of 9 malachite.