This thing has nothing to do with reputation or somethig like that.
Junktown has pretty low density of guards and most of them don't have high range weapons, it's not hard to kill someone with sneak-burster in there. Simply burst some loner, quickly resneak and runaway few hexes so the guards don't find you, then come back loot stuff and resneak, that's it.
It's better to stay away from junktown these days (unless you're a sneaker) and if you really need to go there just try to stay near guards as close as possible.