I'm not voting really. I find it kind of creepy to be honest, but it is a game mechanic. I'm not sure how the lore works. If you outright kill the soul by using it that's pretty evil, even for animals. I like to think it's like letting water through a hydroelectric dam and when you use the gem you release the spirit. I'm probably wrong though and I accept that.
If you destroy the souls to use them honestly I think naming every trapped soul would make me avoid using them, even as a mage. Then again "it's just a game" mentality would probably come in to play if avoiding use of them is actually tedious in the game.