The way I end up with both intrinsically good creatures and basely evil creatures in my world is like so:
Drythen created the world, and in it he created races and the beasts. Take, for example, unicorns and pegasi. Both were created beautifully.
One of the things that happened when the Engast ('angels') rebelled, was that Nuriel (my Lucifer) tried to replicate Drythen's works. However, because he didn't have the power to give life or to create life-forms, he ended up just twisting what was already made, tainting them and giving them a basically evil nature. Going with our previous example, we end up with black horse-like creatures with bat wings and twisted horns who are also carnivorous.
This is the only way I have one of the popular elements of fantasy -evil represented by appearence.
Please ask questons and such to help me figure out a bit more about how this works.

So, is it sort of like what happened in this world? When Lucifer fell, a third of the angels fell with him and he also ruled some of the beasts? Or is it more like the explanation Saruman gives to the orcs in the FotR movie about their origins?

More like the orcs, I guess. Some of the Engast fell with Nuriel, but he doesn't rule some beasts. He corrupted some of the beasts, turning them into a differant race, which he then corrupted. Like the orcs, I believe. I haven't read that in a while.