I actually ran a game with one of the characters as a natural werebear. The character treated it as a Sacred Gift. Wonderful backstory on it and everything. I'm a sucker for a good backstory.
Anyway, it was a bit problematic to balance out every encounter and to keep things completely in control. Good RP on the player's end helped keep the whole thing manageable. I would have loved to have had the leveled template that Sean put together when the campaign started. I think we would have had even more fun and it would have made the character even more unique because a lot of the balance concerns wouldn't have been as prevalent.
As far as afflicted lycanthropy goes, I haven't ever had it be an issue. Admittedly, I tend to shy away from lycanthropes because of the RP concerns if there is an afflicted character. Though, in this last campaign, I started feeling more comfortable with that possibility. However, the PC's always made their saves to avoid contracting the curse. So, I can't offer much helpful advice on that aspect. Still, that doesn't prevent me from throwing my hat into the ring.
Your Con damage idea is a good attempt, but what is to keep the character from just using Restoration to bring it back up each day? That kind of negates the impact I think. Even if they don't do that, you still have to face the fact that may take as little as 3 Con and a max of 12 Con. A major nuisance to be sure, but after the moon cycle, they just need to rest with good health care a few days. Maybe this is enough of an impact, but it seems like you are looking for a bit more.
Of course, you could make it a little more simple. They change to beast form and cannot change back at all until they satisfy their urge. Make it completely involuntary. Then, they need to make sure they aren't wearing heavy armor when the moon rises. Otherwise, it will probably be ruined and may cause some damage. If you remove the hybrid forms and just retain the beast form, they won't be able to effectively use weapons. Magic items will be problematic. Even a simple potion is hard to drink if you don't have thumbs. There will also be problems with communication with the rest of the party.
Now, there will be some people that enjoy the beast form and don't mind staying like that. So, after 3 days in beast form, maybe they start losing 1 point from Cha, Wis or Int. This will drag them further toward becoming a beast. And since this is a curse, restoration doesn't have any affect? (Of course, you could use that with the Con damage too.) When their Will saves start going down and they start losing skills, that might get their attention.