By saying the game punishes you for assassinating people do you refer to the ending cutscene? Because aside from those changes, the game doesnt punishes you, it just changes the final missions to a more grim and dark atmosphere.
I agree that Arkane depend a lot on their lore notes but at the time of Dishonored the budget probably didnt allow for a bigger production scale, and i remember you get a decent enough context out of sneak past the guards and eavesdropping on them.
When you think about it, all Arkane games do that, they rarely put effort into making cutscenes, its just the good old audiologs and lore note and guards or npcs talking about whats happening, its textbook immersive sim, just like Thief, System Shock and Bioshock before it.

Well, a bit of spoiler territory but if you're at high enough chaos Sam will fire a gun into the air, making enemies more alert. Emily could be killed if you aren't careful at the end. And I think a bad ending is definitely punishment alone even if that stuff wasn't there.

I also don't consider Bioshock to be an immersive sim, but those other games you mentioned don't punish you that hard for choices. In Thief, you don't get punished for stealing items. In System Shock you don't get punished for hacking.

High Chaos is the aggressive route so Sam firing his gun almost makes no difference in the end, since you are going to murder your way through anyway, its barely a punishment and more like a challenge-test for what you have been doing with your abilities. But if you consider the ending cutscene a punishment then fair enough, although i think its more of a choice and consequence matter than a punishment, darker route leads to darker result, i dont think its strictly a punishment for you compared to being a cause and effect.

I wasn't referring to "punishment" withe the examples at the end, it was to demonstrate that in this subgenre of games they all follow the same formula of storytelling which is audiologs, notes and npc conversation to lay out the worldbuilding and the story to the player, the cutscenes rarely happen and if they do its in between levels or just near the end and at the start.
System Shock doesnt punish you for hacking but thats because the ending is always the same, instead its more of a horror rpg where your punishment comes from resource management, and in Thief from getting caught since its more hardcore stealth game than Dishonored which is stealth action that gives the player absolute power over everyone.
Bioshock may be less punishing but thats because the morality is very simple in that game, even worse in Bioshock 2 where the good choice leads to 100 less Adam which is like nothing to be sad about.
Dishonored blurs the lines better than Bioshock, the granny quest in the first level puts you in a situation where you need to choose between acquiring runes or serving a gang leader which later has a consequence on how you approach another level, that choice and consequence system is far ahead of Bioshock in my opinion.