Before I get into this, I'd like to establish the definition of "good" in the context of Skyrim by using the definitions provided by the Nine Alignments System.  That way there's an objective jumping off point that most people are already familiar with.

Good characters and creatures protect innocent life. Evil characters and creatures debase or destroy innocent life, whether for fun or profit.

Then there are the three types of good alignments: 

Lawful good: A lawful good character acts as a good person is expected or required to act. He combines a commitment to oppose evil with the discipline to fight relentlessly. He tells the truth, keeps his word, helps those in need, and speaks out against injustice. A lawful good character hates to see the guilty go unpunished.

Neutral good: A neutral good character does the best that a good person can do. He is devoted to helping others. He works with kings and magistrates but does not feel beholden to them.

Chaotic good: A chaotic good character acts as his conscience directs him with little regard for what others expect of him. He makes his own way, but he's kind and benevolent. He believes in goodness and right but has little use for laws and regulations. He hates it when people try to intimidate others and tell them what to do. He follows his own moral compass, which, although good, may not agree with that of society.

From the UESP on the Soul Cairn:

When a soul is captured by a Soul Gem, it is transported to the Soul Cairn to roam for eternity.

This is true for humans and non-human animals.  Without turning this into an animals rights debate, I'd like to put forward that it is still morally wrong to submit an animal to the Soul Cairn to roam for eternity.  How much worse it is, is another discussion.  

Now that that's established, I ask, how can any character that claims to be good justify practicing, or supporting, Enchanting?  By "supporting", I mean buying soul gems and enchanted gear & weapons.  It's supporting the market for soul gems by providing the demand that keeps up the supply.