I've thought about this a lot. Really, why have I spent so much time thinking about it? I should be doing better things with my life.
It depends on my characters' point of view, which comes from their life experience. Some characters see enchanting as strange wizard crap. They have no idea how it works, only that it does. For example, I had an Imperial rogue-type guy who would glady use enchanted weapons, but if they ran out of juice he'd throw them away. He didn't know how to fill them back up. It was all mystical hooey to him; he only saw the effects.
One "good" mage character rationalized it as temporarily using the soul. Once used,it was released to continue on its journey to wherever it was going. He thought the soul couldn't be destroyed permanently.
Most of my characters do see it as evil, wrong, unnatural, dishonorable, or even disrespectful. They have varying degrees of understanding of it, but know there's something nasty about the whole business. So most of my characters are weaker than the game intended, because they refuse to use enchanted items.
Then there are the dragon souls. What happens to them? The "good" (have to put good in quotes because something, something, whole other post) dragonborn characters have really just found the thought of absorbing dragon souls too disturbing to think about for long.
Me, as the player, I just think enchanting's a bit overpowered. And I can't be bothered to do it most of the time.
To answer your question, my good characters that use it rationalize it like people in real life rationalize doing slimy things. "Eh, it's not reeeaaally hurting anyone." or "It might be sorta bad, but I'm doing it for a good cause." Or they're ignorant of how things work or ignorant of the consequences. Also like real life.