Alternatively, Spooky doesn't want Roko lashing out at anyone in her depression.
It seems to me to Spookybot's appearances tend to be when an AI is in a moment of a crisis of faith or when they are on the verge of an emotional breakdown. When people are under extreme emotional distress, they lash out at people, they react in a chaotic manner. So from there, we might believe that Spooky intervenes just before that point where an AI might hurt someone. While they might hold some disdain for humanity, Spookybot might be the thin, creepy line between coexistence between Humans and AI, and, well....war.
Notice that the main times they appear are when Bubbles is looking to find her memories, when Roko is having her crisis of faith about the justice system and now during her disconnect between her and this new body. These are all points where someone in extreme distress/pain could end up doing something they could end up regretting later on. And given how Spooky has multiple chassis, I imagine they are constantly on watch.