The Pathfinder Online team has posted a long and very detailed blog article about how the alignment system will work in the game on release. According to the post, alignment has been one of the most keenly debated topics on the forums.
During character creation, you can select your character's core alignment. This is basic standard of behavior your character strives to maintain at all times. In fact, the game assumes that your character routinely thinks, acts, and behaves in a way that supports this core belief—there are countless minor events and interactions every day that the game can't detect that provide your character with the opportunity to act his or her alignment. While you may deviate from this standard, over time your natural tendencies assert themselves, and you slowly return to this core alignment. You can change your core alignment at any time, but you can only change to a new core alignment that matches your active alignment.
Read the full post on the Pathfinder Online site.