High Overseer's fate.
Okay so it's not okay for them to disgrace Corvo, but it's perfectly fine for Corvo to effectively do the exact same thing? Even if he doesnt kill ANYONE in the entire game, such an action would seem hypocritical. And letting the guy live, but disgraced doesnt really seem any better than ouright killing him.
Also, they simply took the branding at face value? No questions whatsoever? Overseers either lying dead everywhere and/or other Overseer's waking up with no idea how they fell asleep. The High Overseer being found unconcious by himself with no one who could have performed the branding to be found. I'm pretty sure for such a sentence, some sort of official review would have to be held. Nobody thought to ask his superiors if such an order was given?
With all the evidence, you'd think the concept that the High Overseer might have been knocked out and branded by the same person who either killed and/or knocked out all these other Overseers should have occured to SOMEBODY, even if the organization is corrupt. Rules may be rules, there ARE instances where they don't really apply and need to be considered. That's just basic common sense. Even for an organization run by jerks.
Yeah, the guy was a douche. I get that. And Justice of some sort has to be had. But the lack of even the most rudimentary of critical thinking really makes no sense. At least the nonlethal neutralization of the others made sense