This is covered more in the GM section of the Organized Play guide. Players are expected to contribute to a positive playing experience at the table, including avoiding evil acts. The PFS guide articulates this in a beautiful and direct way:
Players are responsible for their characters’ actions. A player’s perception of what their character would do in a particular situation is never more important than the experience of other players at the table.
Infamy and Alignment
The in-game solution is Infamy. When characters perform evil acts, or other inappropriate things (such as inappropriately deviant or criminal acts) the GM can award them Infamy points. A character with 3 Infamy points becomes evil, and thus inadmissible for Society play.
Lower levels of infamy have more moderate consequences, such as limiting the level of equipment they can use.
GM-Alterations to Game
In some circumstances, evil activity is relatively small and driven by the story. In Society play the GM is encouraged to make story-related changes to encourage a welcoming environment for all players.
Although this didn't match your description very well, it's worth noting that the GM does have this kind of discretion in their toolkit for managing evil activity.You can read more in the Table Variation section.
Removing Disruptive Players
A more extreme situation occurs when the player is the problem, rather that the character. If the evil activity is disrupting the game or making other players uncomfortable, the event organizer can eject the player from the game. There is a reporting chain, and it may involve review by venture officers. See Community Standards for more info.