Sure it does. And it does so explicitly in the case of every creature other than humans.
From the 3e MM p. 12. "Alignment, this entry giest hte alignment that the creature is most likely to have.... Usually: The majority (more than 50%) of these creatures have the given alignment.
Now, I suppose I'm carrying my analysis of human society over from the days of 2e when humans actually had a listed alignment but in most societies it would be "Often neutral."
In no case, is human society likely to be more strongly alignend than "Usually X".
So, from your interpretations of alignment guidelines from two outdated editions, along with your personal assumptions about the ethical systems normal to humans in pseudomedieval fantasy worlds, 'evil' doesn't mean "evil enough to deserve death," because that would mean too many people would deserve to die.
That's ridiculous, but okay: what percentage of the population does deserve to die, then? I mean that if four out of ten people commit atrocious murders, do you only execute one, because forty, thirty, or even twenty percent of the starting population would be too many?
You want to formulate an ethical reductio ad absurdum: evil can't always mean 'deserving of execution' because the consequences are ethically unacceptable: too many people would deserve execution.
First, this is wrong, because it relies on false premises: you might prefer that all human D&D societies enjoy the same distribution of alignments among their populations, but, unfortunately, your preference does not make it so.
Second, it doesn't follow from the fact that, say, thirty percent of the population deserves execution, that thirty percent of the population will actually be executed. There is no ethically unacceptable conclusion here.
I believe the problem with the reasoning in this debate is that it's moving backwards: the rules have already established that those of evil alignment (and, yes, often neutral) deserve extra violence, if not death. That's the foundation. If a particluar NPC's or PC's deeds don't merit all of the consequences attendant to an evil alignment, then he's not evil. That's black and white, and it is precisely the reason why Detect Evil is a licence to kill.