I was explaining my thoughts on this as pertaining to my scifibigbang fic to my mother, who pointed out that a werewolf is a very poor choice for this. Her reasoning was that a werewolf, whether s/he likes it or not, does turn into something very, very nasty once a month (providing that s/he hasn't taken Wolfsbane, of course) -- someone with a mental illness or disability, or a homosexual, has no inherent violence/nastiness. Or, rather, they have no inherent violent tendencies because of their illness, disability, or sexual preference.
Thinking about the issue in this light almost paints Rowling as subtly saying that there is something inherently wrong about these people. Admittedly, I've never thought of Rowling's approach to lycanthropy in this way, but maybe I'm too involved with the characters themselves. I think that Rowling definitely should have picked a better target -- an elf, maybe, or a centaur? A creature/person that has no inherent violence, whether under their control or not, but which society by and large still mistrusts, fears, or is suspicious of. However, I still think that werewolves, on a whole, are a good candidate, despite this slightly worrying take on things.
My reasoning for this is that I choose to believe Rowling intends the comparison to be made on the grounds that a werewolf doesn't get to choose whether or not they're afflicted (generally -- I have my suspicions about Fenrir Greyback, but that colours the issue dramatically), much as a homosexual or a sufferer of an illness or disability doesn't choose their situation. Additionally, choosing an elf or centaur would not necessarily highlight illness or disability, but perhaps racism, sexism or other prejudice of that manner. Which also makes me think that this is the reason that Rowling has not specifically said that lycanthropy (Lupin's, specifically) is a representation of the treatment of homosexuals by certain aspects of society.
Anyway -- thoughts?
That was ridiculously rambly, I do apologise.