I don't think it's that there wasn't any dissent, but rather they were able to work through it, for the most part, peacefully and fairly. It's probably why debate and rhetoric appeared to play a considerable part in their society; not only was it an integral part of their culture and education, but it also functioned as a way to communicate and understand one another through disputes and disagreements. There are even two Amaurotines "arguing" about foreign intervention in the side quests that take you through the city, but it's presented as friendly discourse. In both Amaurot and Elpis you can also see there were all manners of Ancients, some friendly, some snippy, some arrogant, some odd, happy, irritated, sad or otherwise, so it's not so much of a matter of suppression as the communal mindset of working through differences and setting aside petty personal vices and vendettas for the sake of the wider picture. Which I don't find difficult to believe in, personally, but YMMV.
I'm guessing you mean post-Sundering. And I'll say again, the answers you're looking for are already there for you if you look closer - Emet was clearly plagued by moments of doubt and in a difficult place of both actively looking for a reason to be freed from his awful mission while simultaneously feeling completely beholden to it, to the point that he took it upon himself to immerse himself in living as a mortal to find a reason for their survival (and failed.) Lahabrea grew reckless and effectively lost his mind in pursuit of their goal, and Elidibus, being part primal at that point and wholly in service to Zodiark, served almost as a cattle prod to keep them on track. They were gradually broken down in individual ways over the eons by what had happened to them, their isolation and the weight of what they were trying to achieve. I think Emet did realise it was futile in the end, but his devotion to his duty still meant he couldn't let go unless he was stopped. The other two were too far gone, and I don't find it at all hard to believe that their love and sense of duty towards their people blinded them from seeing any other path. It's funny how you feel so much for Hermes and his sense of isolation, but conversely expect so much from them under such circumstances.
I disagree on what constitutes "cruelty" and "indifference" here, on what I'd call a matter of ignorance. And of those who met Hermes and his point of view, almost all were sympathetic and trying to help, including one of the Ascians themselves, even if they struggled to know how. By all accounts, I think part of his problem was his reluctance to reach out, because we see the Ancients demonstrate a capability for growth and change when actually given the opportunity to.
It's almost nostalgic, huh?