I feel like I say this in every thread like this, but part of what makes NPCs a threat is that they have useful, even essential skills that other people rely on. Things they can't do if they're dead, or on drugs, or in prison, or whatever. Things that give them leverage when they're following their parts around.
This isn't big city living, you can't just kill anyone you like and assume someone will step forward to take their place -- if someone does, usually they'll be worse at whatever it is, and probably trying to take advantage of the situation to boot.
The Quarantine wants a gang, but he can't have a gang if they're all dead. Every person he shoots is one less person in his army.
The PCs decide to stone a slaver, sure of course. But people depended on that slaver, for better or worse -- there's a hole where he used to be. The slaves he provided were used for something, people relied on that, so now what will they rely on instead? How will they cope, and what about the ones who can't cope?
Marser chops off Jackabacka's hand, that's a twofer. Jackabacka needed that hand for all sorts of shit that she does for the community. And Marser does something too, so just killing Marser means that that shit won't get done anymore, either.
I mean, like DannyK says, there's nothing wrong with PCs going on murder sprees. It's up to them. They decide: who survives. What survives? What services, what skills, are essential enough to put up with the people who have them, and what those people want? Maybe the PCs will decide against compromise, maybe they'll decide that their future doesn't need slavers, or engineers, or farmers, or drug-addicted gang members or authority based on anything but fear and violence.
That's fine. That's what you're playing to find out. And it's your job as MC to make that real. To figure out what it's really like, living in a world where the guy with the scary army murders you if you talk back, or where people get stoned to death in public, or cutting off somebody's hand means losing your head. Because people react to that shit -- it shapes them, and their decisions, and what they want and what they think they can get out of life. And I don't mean your job is to make everything 'realistic' or gritty or terrible -- you make it real within the parameters of the genre, and the kind of apocalypse you want to be playing in. But even if it's a cavalier world of Mad Max adventure, people still react. What the PCs decide matters, nobody just yawns it off and goes back to life as usual. Because there is no life as usual.
So I mean, I'd say just think about that. Think about what these people are worth, to the community, and also think about how they react to things, as individuals. Those two are always going to be in tension, but it's never really your job to resolve that tension -- that's the PCs' job.