I don't think there's a need to be so binary. You can think Amaurotine society was broadly good but still not believe it was perfect enough to justify the Rejoinings (if it's even possible to have a society perfect enough to justify the mass murder of sapient beings for), just like you can believe it was broadly bad and still not think it deserved to be exterminated. They're not superior, they're just a group of people. No more or less.
As for Hermes, like all renegades, he both is and is not a product and an indictment of his culture. Because human nature is self-contradictory, even the best societies will have a marginalized population at the periphery who are nevertheless products of the cultural core in their own way. Hermes is a shadow of Amaurot at large, possessing a nature that is unsatisfied by and rebellious of its values while still unconsciously replicating them at their worst. Amaurot encourages a unique (if not fundamentally remarkable) sort of conceit towards non-human life, one which Hermes indulges in constantly, until it becomes warped by his nihilism into conceit towards life in general.
Is he 'Amaurot's fault'? It depends on how you look at it, but in my (unhappily-held) opinion, it's idealism to think that a world where everyone is happy can be achieved just by balancing everyone's needs carefully. Whether by choice or sheer inertia, social resources are allocated based on general necessity. The empathetic muscles of Amaurot that could have helped Hermes (or people like Blaste, or hell, Athena) atrophied because the overwhelming majority of people were content. Could they have been made stronger without the rest of the population having to suffer proportionally? The story offers no suggestion that they could - the Final Days and the Sundering 'improve' the world for people like Hermes by spreading misery to everyone, and though a more subdued change would probably have also done the job, it would have still required a shift in collective experience - towards grief and loss.
Society can be optimized to marginalize and hurt the least amount of people, but once you get past that, it's a zero sum game. Again: Human nature is self-contradictory. Unless you control the natural variance of the human mind itself, some types of human minds will be unhappy. The individualist will chafe in a conformist world no matter how nice it is, while the conformist will feel aimless and lost in a individualist one, and this is true for countless other situations.
When it comes to forging the world we all have to live in, it's 'kill' or 'be killed'. In this one sense, at least, Hermes cannot be blamed.
This feels a bit silly, but as another autistic person, I have to agree I'd prefer to live in Amaurot than anywhere else in the setting. It's not even that I'm conformist - it just obviously has a much higher quality of life than all the other places. Amaurot is a society that is built contrary to what I'd personally want, but is nevertheless optimized way better than the alternative, in the same way than I'd much rather live under a modern dictatorship than in a free society in the middle ages. Even taking the most cynical approach to the setting, I'd much rather sulk at the fringes of the Unsundered World with my one or two other deviant friends where they probably have computers and I could conjure a really nice house and good food for myself every day than, I dunno, die of dysentery in Ul'Dah.
Anyway, putting that aside, I have to say I'm pretty surprised you listed Sharlayan as the alternative, since it's basically Amaurot but in the Sundered World, minus the robes (though there are still a lot of robes). It's a pretty conformist, conceited culture that sees itself as having a special role in terms of the rest of the planet, and has a lot of firmly-held ideas about how its people ought to live. All wrapped around a culture of scholarship and resolving everything through civilized debate. It even has the Greek! And the creepy giant magic science zoo!
You just don't get to be hot for 10,000 years.