The important point to be made is that this doesn't risk the 'we still need evil things to fight' problem
Is that a problem though? That we need "evil" things to fight? Can't our opponents simply have another perspective than ourselves without being tagged evil for the race or culture they come from?
I still agree with you that a main character Yuan-ti pureblood would face prejudice and fear from many populations based on history etc but I don't agree with you that the fear and hate based on prejudice or general conception of a race is a crucial element. I don't know the general age demographic for dnd players but surely the majority should be old enough to understand moral and philosophical concepts that goes deeper than "me-good you-bad because someone says so". What is an evil-inclined society? From who's perspective and do members of that society share that?