In Lies of P, there is a group of NPCs called the Stalkers. More specifically, there are two kinds of stalkers: the Bastards and the Sweepers. The Sweepers are an organization of guards for the old families of Krat, while the Bastards are an organization of guards for the Alchemists and the Workshop.
Why is that information relevant? Well, the Bastards and the Sweepers react differently to Pinocchio based on his Humanity points and some might become very hostile towards him if side quests have not been completed and dialogues have not been exhausted.
This is the case of the Atoned and sadly if they have already decided that they do not like you, you have no chance to mend that relationship so fighting it out is the only way.
However, the Atoned will not become aggravated with you if you had spoken to the Red Fox and the Black Cat along with the receptionist over at Hotel Krat.
The reason why it will not aggravate then is because you will be warned of who the Atoned is and how you should act around them.
Additionally, if you managed to speak to the Atoned without aggravating them, hitting them while out of conversation and then walking away will cause them to become hostile and attack you.
Once killed, the Atoned cannot be brought back. During the fight they will inflict decay on the player and once defeated, they will drop their costume (mask and outfit) for Pinocchio to wear.
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