The issue, I think, is that her solution appears not to have worked. People still want to advance, prosper, and reduce suffering. People are still very willing to turn to Primals for salvation - Hydaelyn being one such example - and even without them are wont to turn to individuals like WoL. At the end of 5.0, Urianger even tells Emet that they share the selfsame motivation, creating the "best of all futures". In this context the sundering did not change the nature of mankind, it merely set-back their progress.
The Convocation should not have even been her enemy, she is the one who made herself their enemy, by intent. I can hardly view her attempts to reach out to them as being in good-faith when any argument she made could only have been predicated on lies about their situation.If her only interest was to create the Sundered, then it would be counterproductive to alert the Convocation that you disagree with them as you potentially just give your enemy more time to act. No, she genuinely wanted the Ancients to live on whole, her attempts at reaching out to others and pleading with them to change proves that.
And this was a very good decision on Midgardsormr's part. He didn't presume to be the arbitrator of his entire race's future and dictate what path they should take, he took his own path divergent from their own. I think Venat should have done the same.On the dragons: In the quests in Ultima Thule, you find out that Midgardsormr was widely mocked for his decision to flee and that is why he was the only one t make the journey. Midgardsormr had the answer, for sure, but his answer brought him to Hydaelyn/Venat and away from the Dragonstar.
It doesn't appear as though Hermes was strictly in violation of any rules in creating Meteion. All creations don't necessarily need to be accounted with the Bureau, rather people do so in order to widely distribute their creations. On Elpis, given it was specifically for the creation of new lifeforms which might one day be seeded across the star, it looks like registration is mainly for creations that pass testing and are ready for that. Meteion, however, was basically Hermes familiar and a personal creation, and as such probably didn't need registration. However his plan to create hundreds of her and send them across the universe was probably breaking the rules on so many levels that this is why he chose to do so in secrecy.