I think it's childish to assume the writers either wouldn't believe that Venat's actions would constitute genocide or that they would condone that action. But that's the point, the story is not that deep, the writers didn't think about it that much (also incidentally a Yoshi-P quote: "We didn't think players would think about it that deeply" with regards to the Elpis timeloop). And they show their hand constantly in the story, disengaging you and yanking you out of a state of immersion.

It's a Kingdom Hearts level story that needs to exist so that the game has a story. There is not much the writers had to say beyond "everything will be fine, we are here for you during Covid". No more, no less.

Let me go a little bit more into detail here. The story is written with the end in mind first and then everything up to that point is done so that it fits without much regard for characters or the like. What was the end goal for the Elpis timeloop? So that the previously unknown character Venat/Hydaelyn would share a bond with your WoL that spanned the ages. That's why it's not an alternate timeline. That's why she had to retain her memories. That's why Kairos was invented, a literal mindwipe device that exists just so the timeloop roughly makes sense even though it shouldn't even exist based on the Crystal Tower's prior function in Shadowbringers. So it's not like they wrote Venat's character beyond "I love the land and the people and I want them to be free". They didn't ask "What would such a person do in this situation" or "how with these parameters in mind would the story organically evolve from here". They asked "how can we make it so that the world evolved the exact same way it did, that she did everything that was established prior with the whole sundering the world thing and now simultaneous sharing of that new knowledge and bond with you". And since there's no good answer for that they had to give us bad answers that crumble under scrutiny - they should have arrived at the conclusion that the timeloop was a bad idea, but that's not how they operate. They had to have a timeloop and so they made it happen against all logic.

Why do you think Fandaniel claps before Zenos can kill a character in Garlemald? Well because they wanted to have a hype duel with the WoL and Zenos at the end of the storyline. And had Zenos killed for example our friend Alphinaud it would have never been hype. It's not that complicated. Also major character deaths are in general not appreciated in the writer's staff, I think that's pretty obvious since Y'shtola was sliced in half by Zenos at the beginning of Stormblood. Again, just think of the writers as having clearly defined goals first and then trying to write the characters and plotlines that lead there so as to fit those goals later with varying degrees of success.

So take the story for what it is and use your knowledge to tell better stories yourself. Or worse/equally as bad stories. The best thing the story can do for you is inspire you not just in spite of, but because of all it's shortcomings. That is the true message of Endwalker for me personally.