So basically, we've got approximately four possibilities on how soul gems work:
Theory number one is kind of like recycling, where we trap a soul, use it, and it goes to whatever plane it was meant for. Well, that sounds pretty inconvenient but not too bad. I can imagine it must suck though if the person never really gets around to using it. This theory isn't canon.
Theory number two is basically that the soul is completely used up until it's nothing. In short, fucking evil.
Theory number three is that soul gems doesn't take souls, it just takes a portion of a beings essence and releases it. This is the best option.
Then there's soul cairn,the canonical answer to this question. Which in my opinion, is probably the worst. It just doesn't seem right to me that someone can get sent to purgatory because some stupid prick decided to absorb their soul. Even to an animal I wouldn't think this is justified (which raises the question, where does an animals soul go, anyway?) My only question now is whether the writers of the Elder Scrolls series thought this much into how soul gems work.
As for the falmer, morally even taking their souls would be a morally abhorrent act. Don't get me wrong, I fucking hate the falmer and they ruined an entire game for me once (I found an area that I couldn't just exit when I was a low level and they raped me) but if you think about it, you can't really blame them for their evil. They were twisted into the creatures that they are now because they were killed off, enslaved, and poisoned. If anything, the Dwemer and the Nords deserve to suffer for these crimes, not the falmer. As for the fellow that proposed the theory that the falmer's soul degraded with their fall from grace; I find it makes sense.
So, looking back at the crimes of man and at the purity of an animal *Really, do you think a Wolf attacks you for anything other than food?* I would actually argue that entrapping the soul of man or mer is far more justified than that of an animal. I mean, a Fox definitely didn't create the falmer.