I'd look at using a system where the were-players have to regularly save to avoid giving in to urges, but if they fail, it's the equivalent of magical compulsion in terms of alignment change - they will probably not be changed if they resist it.
Something like full moons, good food and drink, and so forth might be triggers, and unless the PCs can make a Will save against a DC of (10 + half their save modifier + situation + resistance), where resistance (modifier of -5 for detestable actions to +10 for something they have no problem with) is how much their characters would defy it on a personal level and situation (modifier of -10 for horrible targets to +10 for an ideal subject) is based on how the well the target suits the compulsion, they have to react.
A were-PC (Will +16) is alone in a dungeon and is hungry. He wants to eat, but there isn't any food left. However, he finds some human prisoners. Cue an urge to eat one, the plumpest of the lot (+5 situation), which fills the character with horror (-5 resistance).
DC (10 + 16/2 + 5 + -5) = 10 + 8 = 18, a fairly easy save for this character as cannibalism is definitely not something most PCs would even contemplate. The player rolls 12. The character feels the urge but can keep it in check.
However, he later finds some spoiled meat. It might make him ill, but his were-rat self wants it. His save gets a +2 situation modifier as the meat doesn't look/smell too bad, and a +6 resistance modifier as he is now much hungrier than earlier.
DC (10 + 12/2 + 2 + 6) = 10 + 6 + 2 + 6 = 24, a slightly harder save. With a 6, the player fails. His character tears into the meat, ripping at it with his hands.
Of course, a player can decide not to resist an urge. This system is intended to make players more aware of the potential dangers of lycanthropy rather than take control of their characters completely. If they are constantly making forced actions, I'd suggest changing the modifiers slightly.