You wont get back your ingredients when undo any enchantment, but you will learn that enchantment you disenchant if you havent learn it.
I dont know the total of malachite gems in the game, but now I only left keara's fortress and hall of echoes havent explore yet, and got 8 malachite gems in hand. There a quest which required to turn in 2 malachite gems, but I havent go pick it up yet. If I complete it, then will have total of 6 in hand. Well I keeping them for enchanting lvl10 healing aura in accessories.