@Anzuda
Most of your issues come from the fact that a nation as a whole has to have a single ailment really.
it doesn't answer why the saint is "Good"
Well, we haven't seen enough of her to be totally sure, but my guess is that she was ok with killing them because they posed a threat to the people she was charged with protecting.
From her chant ( assuming they really are her true feelings and not just glorified mumbo jumbo ) She does consider them human, but she condemned them to death because they did not repent their sins.
Basically, she killed some heretics who refused to repent and was a threat to her people, because it was either killing them or letting the "innocent" people die.
The main reason she killed them was that they did not act as they should have, they burned villages and killed people, and so it was their "punishment".
If I had to guess, She is probably"good" because
she needs to fit the Saintess theme she does not enjoy killing and supposedly avoids it at all cost as she values life highly and helps those I need.
Also, this is just a theory, but at the end of the chapter, she says to herself " I have to save them"
this could be referring to literally anything... but its possible considering they were just talking about the cursed forest that she wants to save the dark elves who she knows was exiled there from "the evil" that she suspects is inside the forest. ( could be a reason for conflict with the MC at first )
Or she is just talking about the people of her nation that she needs to protect from the big bad evil guy that´s inside the forest before he comes out and kills everybody like the big bad evil guy he is.
Why is it fine for the so-called "Good" to prosecute the dark elf?
Just because the nation is good-aligned doesn't mean everybody inside it has to be good, but yeah this is a problem if you are going to pull everyone into the same group...
If I had to make an excuse to justify the persecution, it would be something along the lines of calling them impure or corrupted etc... but yeah its a dick move for sure.
Also while its a minor difference, it was the other elves who exiled the dark elves, not the humans ( there are two ruling nations on the "good half" of the continent, then human and the elf nation )
the moment the dark elf meet Takuto, they instantly think that he is the incarnation of evil
This is because his aura literally makes him look like a black mass with a human shape and glowing eyes, only his champion can see his true self and everyone else sees him as a monster.
That combined with the fact they know the stories about the ancient evil "The King of Ruin" who is sealed in the forest makes it a pretty easy thing to assume he is a manifestation of evil.
This is also why they are super confused about his friendly and peaceful behaviour later on.
( ofc this is just speculation on how "good vs evil" type of nations usually behave )
He probably doesn't act much like the people from the "evil part" of the continent who thematically might be barbarians and rules by a might make right system.
Or it's possible that the evil continent is like the Dark Elders from Warhammer 40k who is a race of evil space elves who enjoys torture and killing people.
the moment the dark elf join Mynoghra, it was also depicted that their anger for their prosecution is amplified.
Again this is the biggest problem with having entire nations belonging to a set alignment as its highly unlikely that
everybody in an entire nation would be off the same aligment.
We know that the MC does, but it's possible that other rulers also have an influence of peoples behaviours, but the aura is not enough to prevent bad people from existing completely.
The veteran holy knight, for example, is an asshole, my guess is that it empowers the feelings of its leaders' alignment ( good people does more charity while evil people gets more selfish etc )
But it does not stop people from the other alignment to exist, just like the people she killed who supposedly killed and pillaged the village of the presents who asked for her help.