I must have gotten the ED and DKS guide confused, I thought it was mentioned giving the gem away to the Goblins made you no longer get skillpoints, yet you advised to do so in your DKS guide.
But yeah, if it gives 2 skillpoints instead of 0, it's definitely a good deal to get these gems.
I recommended choosing Radcliff as your enchanter in DKS because he always gives 2 Skill Books now, you get to keep Raze's Cuirass instead of giving it away, and it presents the opportunity to trade 1 possible upgrade for your Workshop for 2 Malachite Gems. I didn't recommend doing the gem trade, just that it's one possible perk for choosing Radcliff over Wesson.
Since neither Enchanter offers a unique features in and of themselves, their quests are the entirety of the choice (outside of aesthetics, like personality). At least with others, you choose one feature over the other (melee vs. magic armor for Necromancers, allan brew vs. free potions for Alchemist, and melee vs. magic skill discounts for Skill Trainer).