This thread is going to devolve into The Same Goddamn Argument and three people are gonna spend twelve pages brow-beating us about Venat being bad. But we're not there yet, so sure, I'll play ball; let's discuss the hypothetical, as fairly and accurately as we can, while looking at all the facts we have and dismissing none of them unless they are well and truly irrelevant or disproven. Since this is gonna be long, I'll try to format this as digestibly as I can.
The Problem We're Solving:
Theoretically, there are three potential 'killing blows' in play on the Ancients: if Hydaelyn didn't sunder them, the Convocation were going to sacrifice an unsustainable amount of the planet to Zodiark to keep trying to fix what broke, leading to a situation not dissimilar to the Nibirun. But if Zodiark's not there, the End of Days gets them and we just get a dead world. So, there are essentially three bombs to disarm here, and you have to review the conditions that led to all three.
Because of the End of Days, I see Zodiark and Hydaelyn as essentially inevitabilities in their situation; if the End of Days happens, then some equivalent of Zodiark would happen to stop it... and then some equivalent of the sacrifices would happen to try to turn back the clock, which would then lead to some equivalent of Hydaelyn getting them to knock it off. I don't think any amount of rearranging the variables that lead to Zodiark and Hydaelyn actually gets you anywhere at all in 'saving the Ancients'; in fact, you could argue that Zodiark and Hydaelyn are the best Zodiark and Hydaelyn they could've been; when faced with two questions with no good answers, they're the least bad ones you could produce. So, we have to go to the root: the End of Days. If you can defuse that before Zodiark happens, then nothing else needs to.
So, how do we fix that?
Well, if you'll forgive the play on words, you can't do that once the bird's flown the coop: this is the explicit position Venat describes being in, the Ancients as a society just aren't well-suited to handling this information or situation. In a very real sense, the End of Days is their worst nightmare, the thing that preys on all their weaknesses. So, we have to close the coop; we have to somehow ensure Meteion never breaks bad. That actually means starting before the WoL even arrives in Elpis: the moment to halt is Hermes sending out the other Meteions. If that never happens, then none of those threats to the Ancients ever do.
I don't think you can just stop the launch and then call it a win, though; Hermes will still want the answers to his questions, and will still seek them out. What you'd need to do is to alter his plans. The simplest way to do that is probably to find some way to introduce the issue Emet brings up, early enough to get it factored in: the potential of the negative hypothesis. That he might not get a good answer to his question; the thing that triggered Meteion's turn (and to a much lesser degree, Hermes' own breakdown) was that they were only prepared for a positive answer. But personally, I'm not sure that's the functional idea it sounds like; I feel like the Meteion plan probably had more than one failure point, and fixing the one we saw would've only led them to fall to another. So the better angle would probably be to divert him into a full-on Plan B; an entirely different plan that still pursues his line of inquiry. And then we just hope that doesn't cause an apocalypse, either, which is sadly not a guarantee.
So how do we really fix that?
The best plan, then, would be to solve the problems he saw in the first place. The crux of all of this is that Hermes had a point, he'd recognized a genuine flaw in his society that nobody had an appropriate answer for: 'why do we, as creatures who have transcended mortal existential threats, make creatures that face them'. It's essentially a base theological question from the perspective of gods, he's asking a flipped version of 'why does a good god let bad things happen'. He simply sought to find an answer to this question, and it's just that his attempt went really bad. I think looking at Hermes as the problem doesn't work, because just as a Zodiark and a Hydaelyn were inevitable in their contexts, so was a Hermes, every problem will always have someone seeking a solution. Now unlike Zodiark and Hydaelyn, I don't think Hermes is the best possible Hermes, but we can still solve this in the exact same way; he's responding to a problem, so if we simply solve that problem, he doesn't respond to it.
That's gonna require some difficult societal renovations, but there we have our solution: if Hermes never needs to probe at that problem, the End of Days doesn't happen, Zodiark doesn't exist, Hydaelyn never exists, and the Ancients live happily ever after!
...until Lahabrea goes insane from the Heart of Sabik. Or Athena's resurrection play happens. Or the events of Pandaemonium happen at all without the WoL turning up to stop those dangerous beasties. Or Midgardsormr turns up. Or Omega turns up after that. Or the Seed of Destruction turns up. Or any number of great existential threats the Ancient world itself could've produced that it just didn't, because the skies burned before any of them happened.
Yeah, I'm not actually sure the Ancients get a happily-ever-after here that we're ever truly happy with. That's kinda the thing with solving a problem twelve thousand years in the game's past: they then have to survive twelve thousand years' worth of problems that we know are ahead of them anyway.