I do not believe this to be true and even if I did believe this to be true, 12 people being tempered does not justify eradicating a civilization. At worst it would justify killing the 12 tempered people. If there are Ancients who are against the third sacrifice then that means they aren't all brainwashed lemmings that need to be wiped out like cockroaches. The very point that there is conflict over what to do next proves that the situation wasn't completely hopeless and they were all brainwashed zombies fit for extermination and nothing else.
That would also mean she knew that the Convocation would turn into brainwashed zombies bent on sacrificing everything and everyone and said nothing...Her design is based off Zodiark's, you'd think if the Convocation was so bad at making gods, she wouldn't have modeled herself after him.
If we can't be sure the willing sacrifices would want to be removed from Zodiark and replaced with other life energy from the planet even though we can straight up just ask them because Hythlodaeus is able to communicate with us while in Zodiark. But all these justifications you make to justify why Venat did it has nothing to do with her stated reasons. She wasn't trying to stop the third sacrifice for her deep love of plants and animals. She wanted people to live with their friends and family trapped in Zodiark, removed from the life cycle so that they would get good at being depressed. And given that she did not tell them why she thought they needed to get good at being depressed, it's not surprising they didn't listen to her. She sundered them so they'd no longer have the power to protect the people they loved, so they could learn to live with the pain, like Estinien did. His family being murdered is what gave him the ability to get them past the dragons. So his family being murdered is part of her grand design. You can't understand that and then try to argue she did it all to save some unnamed life energy. When children watching their parents die are the goal of her world, why would she be trying to protect some random life energy that I'm sure you've made sentient in your headcannon to make her actions okay?
That scene is misleading because if they showed the real scene, people arguing in a safe, repaired world over whether to sacrifice cows or not to get their parents out of purgatory and she showed up and devolved them all back to apes in the middle of the debate, we wouldn't be arguing right now. Also even in their fake scene, the people are sacrificing themselves. These innocent people the Ancients wanted to sacrifice who don't seem to exist before or after the Sundering are headcannon.