Alignment, Size, and Type: While a monster’s size and type remain constant (unless changed by the application of templates or other unusual modifiers), alignment is far more fluid. The alignments listed for each monster in this book represent the norm for those monsters—they can vary as you require them to in order to serve the needs of your campaign. Only in the case of relatively unintelligent monsters (creatures with an Intelligence of 2 or lower are almost never anything other than neutral) and planar monsters (outsiders with alignments other than those listed are unusual and typically outcasts from their kind) is the listed alignment relatively unchangeable.
Lycanthropic Player CharactersWhen a PC becomes a lycanthrope, you as the GM have a choice to make. In most cases, you should take control of the PC’s actions whenever he is in hybrid or animal form—lycanthropy shouldn’t be a method to increase a PC’s power, after all, and what an afflicted lycanthrope does while in animal or hybrid form is often at odds with what the character would actually want. If a player wants to play a lycanthrope, he should play a natural lycanthrope and follow the guidelines on page 313 for playing a character of a powerful race.
The lycanthrope template doesn't have anything about changes in alignment or mandatory alignment, so PCs and NPCs don't suffer from them.
In a home game, I would probably implement something like the 3-3.5 check to control your shapeshifting and maintain your norma behavior, but, as no one in my Pathfinder campaigns became a lycanthrope, I hadn't a chance to test what is a good way to manage it.
The typical mechanic (for afflicted lycanthropes) was that during their changes on the nights of the full moon, they generally have amnesia and function as the alignment listed for the lycanthrope of their type. This doesn't apply to natural lycanthropes generally, however. This was spelled out in 3.5. In Pathfinder, they just generalize it with notations on amnesia and misdeed performed.
Otherwise, there's no set alignment for lycanthropes during 'normal' times, though characters that come to revel in the power or freedom of their curse can certainly start to become evil.