Gavinmad
Mr. Poopybutthole
I don't know exactly what goes on since this is my first playthrough but the MC is somewhere between subsector and sector lord as far as equivalent political power level goes, that isn't someone you casually execute even in 40k. Inquisitor Lord or not, the Koronus Expanse is not only not an Imperial sector but travel between the expanse and the Calixis sector is currently impossible so the expanse is completely cut off. The MC is an incredibly important figure when it comes to maintaining stability of the region and executing them with anything short of direct incontrovertible proof of heresy would probably lead to disaster. Now would the MC be in a position to demand the protection of their status extend to their retinue as well? Yeaaaaaaaah that's a bit of a stretch. Yrliet would be doomed, the dark eldar companion (if its possible to have already recruited them by then?) would be super doomed, and Idira would redefine what doomed meant. But maybe the Inquisitor Lord is a secret radical, radicals do rise to that level of seniority in the Inquisition.We should all be executed.
Speaking of Idira...man. Maybe part of it is me not understanding exactly how perils of the warp works and taking unnecessary risks when using her at high veil degradation levels, but on her very first turn on the final boss fight of Janus she fucking explodes and summons a Screamer of Tzeentch that also downs Jae before I can react to it. And then Cassia and my pyro tank MC steamroll the fight anyway. So maybe you aren't entirely wrong about the game being too easy but it seems like the easiest solution to that is to stop bringing Cassia. Or always bring Idira and sling psyker powers like veil degradation doesn't exist and see how much harder you can make things.