Personally, I run with the assumption that she would have still been in Ktitsis anyway. She crossed paths with Hythlodaeus and Emet-Selch entirely without input from us, and the general dynamic suggests she doesn't stick around purely out of obligation, so we can assume that she sticks around, learns about dynamis, Meteion has her crisis, and it all culminates at Ktitsis. Venat's actions in the finale are largely independent, she tags Meteion with the cantrip and escapes on Argos; remember that the WoL's influence on the scene is only on the platform. So she escapes with the knowledge that Meteion is bringing an apocalypse, that said apocalypse is wielding energies of a kind that only Hermes has any great knowledge of, that he specifically wipes his own memory as well to give man a fighting chance (because he knows he'll ultimately side with Meteion, or at least falter in resolve). She also has a means to track Meteion's physical location in space, although no means to do anything with it.
So, from what point, what's the plan end up looking like, and how likely is it she could've come up with it?
- First of all, don't tell the Convocation. Fair enough, that issue comes from Hermes. He openly states that is a problem, and probably knows that better than anyone, especially given he kinda already proved it.
- Only tell select, trusted individuals. Given the attempt to avoid hysteria, and from causing Fandaniel Problems, also fair.
- The Sundering. Definitely the diciest part of the plan, and one she struggles with the resolve of until the second sacrifice. Ultimately multipurpose, as it doesn't just prevent further summonings and weaken Zodiark, it also ensures a population that can interact with dynamis, something that the Ancients couldn't do (and were about to sacrifice the creatures that could). That multipurpose nature does mean there's a few ways to come at it, and at this point she likely had a few allies thinking about it, so while it's an ugly solution, it's one with some clear roads to it.
- Shackle Zodiark. Ultimately this priority likely came before the sundering, but couldn't be performed until after. Ensures that Zodiark's defenses remain, but that Zodiark himself can't be misused. Basically a given.
- The moon as a combination Zodiark holding cell and escape pod. Zodiark does have to be kept out of the way lest unseemly people get ideas, so that makes natural sense. Escape pod as a necessary contingency; thanks to Meteion she knows habitable worlds do exist, so an escape plan in case of failure is viable, and it does need to be big. But it also plants the seed of space travel, for potential saviors to pick up on later.
- The Mothercrystal. Actually not a part of the plan as she heard it from us, and so can't be part of the paradox anyway. It is, however, proof that she's coming up with stuff herself.
So yeah, none of that sounds like something she wouldn't have thought of, especially given she needs to think outside the box. We also don't really have any timeframes to fit anything in, so she had plenty of time to think.
As to how important it is that Hermes remain stable... I mean, putting aside that whole 'Hermes himself made the decision, so maybe respect he had good reasons', remember that he's the one that comes up with the initial Zodiark plan (opinions on the other sacrifices are unknown). Without him, there is no plan, because nobody knows more about dynamis than him, and simply 'questioning him' about the concept would probably take a LONG time and have high chances of missing important facts. Making another expert on dynamis is hard; best just try not to break the one we've got instead.