It doesn't work like that.
For one, you don't have to kill every single guard. Not even close.
For two, a mansion full of guards and nobles is counted towards the same total as a few gang members and plague victims. It's just an arbitrary numerical limit. The game doesn't care who dies or how. It's just X-1 deaths=good, X+1 deaths=bad.
The cities in question are already littered with corpses. They're in the middle of plagues and revolutions.
"I was totally fine with the literal piles of plague bodies and murder victims, but then I heard about a handful of city watchmen getting eaten by rats and that was just too much. Life is meaningless! I'm going to be evil now!"
Plus, like I said, often the game is straight up telling me that I'd be saving more lives by killing particular people since the world is apparently somehow populated by like 40% serial killers.
No the game is telling you that there's consequences to seizing the throne by killing your guards and citizens with the powers of a forbidden dark god.
Also everything in gaming is an arbitrary numerical limit. It's all either 0 or 1 in the end.