A PvPvE Solution
It's gonna sound extreme, but hear me out: if your kill-to-extraction ratio or reputation tips too far toward hunting other players, you are exiled from Speranza and you lose access to the traders, default clothing, stash space and your regular worktables. Instead you move to a rougher underground enclave, which could be a black market camp or rival contrada.
The exile hub isn't meant to be a "punishment" though. It has its own unique crafting tables, its own basic weaponry, special quests and perhaps its own skill-tree (maybe that 4th teal line in the Arc logo?). PvP becomes a genuine alternate path perhaps with its own unique weapons or mods, which would also give PvE players a way of identifying hostile players before they encounter them too - which is a complaint some players have. For example, Speranza exiles would lose the ability to construct conventional shields and augments, so unless they steal them, they would need to make these exile-versions, which may make a unique sound when they recharge. I think along with this they would need to consider limiting the stash limitations some how, so these players don't just hoard 'friendly-gear', although that would be an interesting mechanic.
I think a reputation system would work well and rather than thinking in terms of absolutes, like you kill someone and you are out, the process would need to be gradual because sometimes you get jumped and need to kill whoever attacks you. Anti-player behaviour could be recognised in game by gradually winding back their worktable tiers and stash space as they start racking up the kills. Then once you hit tier 0, you lose the tables, then eventually get exiled.
Lore-wise, Celeste founded Speranza and has dedicated everything to keeping it alive. At some point it makes sense that she, or the traders, would draw a line on raiders who are actively weakening humanity by killing each other instead of doing the job.
Thoughts? If nothing else, it would give the game a bit more depth.