Overall, I agree with the permanently extended claws being synonymous with the evil characters, though there are times when the villains' claws are retracted.
For example, Scar's claws are retracted when he slinks away from Mufasa after Mufasa challenges him. They're also retracted when he realizes that the lion that had appeared at Pride Rock is Mufasa and not Simba. These might just be mistakes, but they both make sense in the scenes they appear in.
In SP, all of the Outsiders' claws are retracted after Nuka dies, and Zira doesn't extend her claws until she notices Kovu and grows angry at him. This makes sense, because even though the Outsiders are meant to be portrayed as the baddies, in this particular scene they aren't doing anything evil, they're mourning the loss of Nuka.
Additionally, though Kovu's claws are initially out nearly all the time as an adult, after the rhino chase, they are almost always sheathed, showing that he's turned into a good guy.
Also, though nearly all of the Outsiders in the final battle have extended claws, the ones that come up to Simba after Zira's death all have retracted claws. This seems to be a sign that they've turned good as well, though there seem to be a couple of Outsiders at Kovu and Kiara's "wedding" that have extended claws. Much confusion.