The "wake up scared" message is most likely not related to robbers, but the spirits being somewhat unhappy with you for some unrelated reason.
The robbers rob you of your valuable stuff, and beat you up (and take your things) if you resist, so I wouldn't call them good guys (if you don't have anything of value, they won't bother taking your junk).
It's a bit of a pity that you don't actually have the ability to beat them up as the quest indicates you might do. The only think you can do is kill them (although I haven't actually tried to knock them all out and leave them, partially because it's hard and risky, as they may wake up and flank you).
As far as I know your treatment of the robbers' corpses doesn't have any effects beyond role playing ones (I leave them for the carrion birds).