That's a good conclusion, I assumed that too so I went the opposite direction and am now allied with the Gray Swan Pilots, doing some non-combat missions.
But if this story wants to tell us that we are actually the ones who are monsters, it is irrelevant because we know it well and we do not need any special signals to become robbers and murderers. Almost the entire on-foot content pushes us in that direction, except exobiology. To be clear, I have nothing against being a monster, but I will be when I want to be, not when some shady organizations like the San Tu State Network and the Pilot Federation want to manipulate me.
But all in all, this is disappointing - because the Halloween event started off really well, with mystery and inexplicable behavior, and instead of continuing in that direction, in the direction of finding and solving the cause, we continue to solve the consequences, with one thin CG, where at first it was not even possible to find enemies. This lukewarm sequel destroyed the good atmosphere of mystery and uncertainty that was created in the beginning.
If FDev can't install that type of behavior into the game, like wild illogical attacks everywhere in Shamash, then they shouldn't have gone that route. This leaves the impression that CG was included hastily, without serious consideration, just to pass the time.