Yes, grannyct, thats the way i see it also...but i just had to do it once!!! hehe
Definately NOT worth giving up the exp for just one gem.
I always use the save/reload at the malachite nodes in Orobas so i end up with at least 3 or 4 gems from a pair of nodes. Sometimes very boring and discouraging but WELL worth using those gems on your high end armor set and weapon(s).