It doesn't matter if it happened "millennia" ago, we're visiting the past in the here and now and interacting with the people she slaughtered even after Endsinger was dealt with by going back in time once again to interact with them for the benefit of the present day Sundered.
Venat's plan is to force the Scions to defeat her in battle or force them off the Star. Her plan entails the Shards will perish and is futile because Endsinger won't stop. All of that is ample reason for them to criticise her either in her presence, or to reflect on her actions later.
There is not even criticism in reflection of any of this as there was with Thordan and the Scions certainly won't stop existing if they ask why she didn't try other methods or view her with contempt. A serial killer can save someone's life though that individual can still be horrified by the fact that their saviour is a mass murderer. Furthermore, we've seen the Scions call out their own allies many times before. The entirety of the game is full of preaching on that front, no matter how mysteriously bereft it is when one of the greatest atrocities present in the setting is revealed.
There's this, for example:
Much as they're willing to criticise their own father they could easily aim similar comments at Venat...
I think you're simply being disingenuous and attempting to build up a straw-man to deflect away from the idea of Venat ever being held accountable in any meaningful way for her actions. It's perfectly possible to acknowledge the crime that is the Sundering without wanting to be unmade or considering the act of unmaking a good thing.
Ishgard faced same issue with Thordan and the church, who both acted as they did to preserve it from the dragons and seeded a noble lie on that basis. Nonetheless, they are still called out for it - by Ishgardians, no less.
The Nibirun situation is judging them for a pre-crime and she never addresses the situation to her people to allow them to confront it. The Nibirun themselves are shown to have hope rekindled in the Omicron tribe quests. They are but one Dead End of many, and one equally open to the sundered, since the Nibirun themselves were once mortal.
The Sundered have many flaws, shown throughout game and expansions isn't considered sufficient for them not to have a right to fight for their existence. The same areas you mention also showcase many of the virtues of ancient society, especially if you do the side quests. It may not be a perfect utopia but it is still a world that has achieved many, many good things.. Whatever JRPG themes the story might think it is aping here, it is ultimately trying to sell a genocide as necessary and there is no two ways about it. Meanwhile the Scions will still aim at the same lofty goals that would presumably result - if we take the story at face value - in the third dead end without a hint of irony