I can't see how were bad guys. Each race follows their own little pseudo religion. The hive have a king God. The vex despite being machines actually have a god they worship and what you kill was just a fragment of that. The fallen have archon priests and high servitors that they rely on to survive. Read why servitors are necessary to fallen survival. The traveler was the God for humanity in this Sci fi and while not all these races are say apart of the darkness, we're all at war. When om Mars, the cabal, a military state was trying to take what Rasputin was defending and a little ghost trying to access it wouldn't mean he'd budge. Your ghost had also said that you needed to find a way to contact Rasputin. Arrays are down and most means of interstellar communication, maybe Rasputin for all intents and purposes has a hard time actually making any contact and instead forms simulation s and protects items of great value across what few planets he can reach