I think whether the ascians are seen as evil comes down to perspective. Yes they are comitting genocide on a regular basis. But you have to consider, they have seen a "perfect" version of the world.The sundering is an unatural occurance and has splintered something that should be whole into multiple parts. It is an anomaly. To use a real life example, if a bout of radiation or an illness fundementally ultered the biology - those who had known what they should have been would look to heal or repair. But those who were born altered and did not know would see themselves as how they should be even though thier chang was due to x reason.
This is the very argument that the MSQ is making. To the ascians the sundered lifeforms are broken and incomplete, something that naturally should never have been. But to those sundered they are "natural" because they have not seen what was before. Worse still is that the ascians can see the hue of a soul and so know exactly who the sundered soul once was, to them they are seeing a friend or loved one who has been altered and broken.
i think Emet's story in shadowbringers was his inner conflict between seeing the sundered life as 'alive' and whole or broken. He was desperate to guage them worthy because then the burden he had carried was lost. To a being that lives forever and has multiple conscious lifetimes, knows that souls are reincarnated again after death, the premature end of their "current" life would not matter overly much. Obviously it is horrendous to those who are sundered and to us who can relate to them due to the natutre of our own existence. Essentially while we can imagne whats its like to be an immortal god like being, we cant really relate, but we can to the ordinary person.
Ultimately when it comes to the ascians they are villains because their method and resolve is horrendous. Their intentions though, I can't actually find something bad in the motivation behind them. They just want to restore the world to how it should have been. Effectively they just want to heal their people and although it is wrong, it is also understandable from their perspective.