I think status rules (Edo Japan, slavery) are a bit different - they remove what might otherwise have been justifications for killing.According to the Code Legal for Waterdeep, Murder comes in two forms: Murdering a citizen without justification: penalty death or hard labor (plus some other stuff and; Murdering a citizen with justification: Exile up to 5 years or hard labor up to 3 years or damages up to 1000 gp paid to victims next of kin.
Note, it does specify citizens there.
As far as historical precendent? Well, in Edo Japan, simply being of Samurai status was enough to remove any charges of murder against someone of lower status. You simply couldn't be accused of murdering someone. And, obviously, anyone killing someone of higher status would automatically be guilty of murder and put to death, regardless of circumstance. So, while not a direct analogue, it does kinda fit.
One could also look at situations where you have slavery, for example too. An owner who kills a slave isn't guilty of anything. A slave who kills an owner is guilty of murder, regardless of situation.
But the Waterdeep code as you present it does seem to have a self-defence rule. I think the most natural reading of that is that justified killing (of which self-defence would be an example) nevertheless triggers a strict liability weregild, with exile or hard labour as consequences for an inability to pay the debt.
To me it does seem a little improbable as a rule, and to be mostly an invention intended to serve a metagame purpose of dissuading players from the use of violence in the course of play.