Well, having half of your fort be werebeasts is, believe it or not, one of the best things that can happen. It's bad news for the other half, though. But anyway, werebeasts heal all of their wounds each time they transform, up to and including missing limbs (I should know, my captain of the guard got his arm ripped off by a werekangaroo and it grew back the following month!), and werebeasts of the same kind won't attack each other. What you should do if you want to facilitate full-fort transformation is segregate everyone suspected of the were-curse, unequip all their armour, and send unturned into the werebeast section with full armour save one body part - leaving off gauntlets is a fairly safe bet. That way, when they are beset by were-creatures, the bites will only break skin on the hands, rather than, say, the jugular. What works best is locking several unturned in a room with a single werebeast, so that there's less chance of them being killed outright.
Alternatively, if you prefer more sanity in your forts, just segregate. Equipping your hospital with individual rooms, each with a door and a drawbridge, means anyone attacked by a weresheep can be locked in until the following month. If they don't turn, they're clean. Otherwise, it's off to the werebeast quarters.
Naturally, if you manage to get them segregated, werebeasts make great soldiers - all their wounds are healed on a monthly basis.