I think the Vigilante class can work well in PFS simply with a couple requirements. First limit the scenarios they do and second make it know to your fellow pathfinders what your secret identity as a vigilante is...they're commiting the same acts of violence and theft so they can't really expose you to the authorities. Especially if your character doesn't commit crimes outside of society missions.
For that matter your vigilante isn't going to seem weird that he changes into a diferent person when social matters end and action is needed. Alchemist pull a Mr. Hyde and hulk out in combat as do barbarians, druids turn into animals...having an alter ego isn't any weirder. Heck going with the social identity as cover for your group and when the action starts, they provide a distraction so the vigilante can change.
Great...now I talked myself into a new character.