It's not surprising that the writers described Hermes as generally impartial. Hermes was a researcher, and being objective was what he did for a living. He was the one who designed the protocols at Elpis, as well developing as Kairos as a means of reassessing species without killing them off. He was also able to recognize that the Iykaones would be a threat to the ecosystem and act on it, despite deeply regretting the decision. If you'll recall, that was the critical test that Emet used to determine if Hermes would be a suitable candidate to rule the Amaurotians as part of the Convocation. It's easy to fixate on his private moments of emotional expression because they're narratively significant and forget that he was well respected by his peers as a scientist.

It's worth remembering that Hermes' rebellious actions on Elpis were not premeditated. He had no grand aspirations for power, and essentially turned Emet's offer down on two separate occasions. He was a clumsy nerd who got himself stuck in trees. The Meteia themselves were sent out simply to explore space and make contact with other civilizations, and he expected to have positive findings. Pretty much any creation with sufficient free will and intellect is capable of turning on you, regardless of how much 'testing' you do, and there are plenty of risky decisions being made in Pandaemonium under Lahabrea's watch. And after the memory reset, Hermes was oddly enough the most valuable Convocation member of them all, being the one who identified the means to forestall the Final Days. Most of his actions on Elpis were done in the heat of the moment.

Emet completely misjudged him, though, and there was an interesting dynamic between the two. Hermes was no doubt aware that the price of his admission to the Convocation hinged on his ability to demonstrate that he was capable of passing judgement on and executing the Iykaones, which is why he was livid when Emet congratulated him and made him the offer immediately afterwards. Hermes' real frustration was over not being able to be true to himself. And when presented with a similar scenario of turning Meteion in to be terminated so soon afterwards, it's not really all that surprising that he suddenly grew a backbone and stood up to Emet. Everyone has a limit to how far you can push them.

I'd be interested in knowing more detail about his life post-Elpis, though. Amon has been kicking around since the Third Astral Era by virtue of body hopping. That would seem to suggest that Hermes had the option of doing something similar but declined to do so, which would be an interesting reversal of his original stance on the issue.