Emet-Selch did completely dismiss our side of things, though? The player character's loved ones, and the billions of lives he already snuffed out were not worth those he lost, he said as much just before the Amaurot dungeon unlocked. We are insects, and he uses us to further his ends however he sees fit, right up to deceiving who knows how many partners to sire children with, children he then also uses for his own purposes. Ascians have never been above cruelty. That moral compass aside, the writers could have used a lot of other ways and words to paint the tragedy of the Amaurotine than calling him a hero. We the player are not his people, the Minstreling Wanderer technically is supposed to be of the First, there is zero reason why he could or even should be seen as such from our point of view. Pity him? Sure. Sympathize with him because we also would totally murder billions of people under the right circumstances, and he words his plan to murder billions more so well? Not so much.
There is one special circumstance with Vauthry: Emet-Selch. He corrupted Vauthry to be a stopgap against the Light overtaking the First too quickly, and hidden in a Hume, it's safe to assume it would be much easier to convince the people of the First to "cease fighting and abandon their ambitions". (Though why Emet-Selch simply didn't just give the power to the Mayor is beyond me.) How he managed to "bring hither a Lightwarden" in the first place to do this isn't explained, and I'd be surprised if it ever was, but since the Ascians needed the flow of Light slowed, it's reasonable to assume they could make certain it would not reach full power until they needed it to.
There is really no doubt that the Warden was corrupting him both physically and mentally long before Crown Of The Immaculate, though, unless there are other fifteen/twenty-foot-tall Humes chilling somewhere we haven't seen yet--Humes that have necks that can twist 360 degrees like the Exorcist (and are disproportionately long when not scrunched), Humes that can digest silverware. That he could function in society is questionable. His speech pattern being meant to indicate he was "off" aside, those Philia-grade tantrums were not a sign of a healthy mind. He was isolated in the Emergent, he never left it, and the citizens of Eulmore seemed happy to accept anything he did, so long as it benefited them in the end. The trial's music is even titled "Insanity".
No matter who is more logical, better spoken, or has the biggest plan, it still doesn't change the fact the writers chose to condemn one of Emet-Selch's victims far harder than they did Emet-Selch himself. I mean, it's great if this is a sign they are learning to write more nuanced villains. But they're going to have to spread that around to everyone to be more convincing, and not make it seem like it's just a case of the fandom darlings having a license tokillbe heroic.