Him admitting that her torture machine did in fact work is not the same as saying I'm fine with you eliminating my species. People grab so hard on that Emet-Selch admitted their tendency to just plow through any problem with overwhelming strength probably wouldn't have gotten them to the edge of the universe to teach emotional regulation to a bird and jump from that to therefore it must have been okay to eradicate his race and create a new species specifically to be tortured...
Given us mere mortals can come up with a dozen ideas better than Venat's torture machine, had the Ancients been given the actual information about the problem, I believe they would have figured something out. But unlike Venat, I actually believe in man's potential and their ability to find a way forward.
Also, even if that was the one and only way to save the universe, I still wouldn't have condoned it because respecting a person's autonomy is my highest moral value. Perpetuating the species isn't even on the list. If all humanity decided to stop making babies tomorrow and I had the power to magically change it, I would not override their will and force them to have kids just so "something" exists. We all know that the universe will eventually end. Taking away people's right to choose just so there is something there to see the heat death of the universe runs contrary to my morals. Especially when making sure 'something' survives involves crippling the people in question.
"Our plan to save humanity involves three month lifespans that you'll spend in agonizing pain." If the species decided it wasn't worth it and to just peace out, I'd let them. But that's because I value people's rights to make decisions about their own lives. She butchered her species and ran them through her despair machine without consent. And given this was a species where half of them volunteered to sacrifice themselves to save the other, I feel like if she explained her plan and the reason for it to them, she'd have probably gotten enough volunteers to be run through her torture machine that she wouldn't have had to take them by force.
ETA:
The only way I can reconcile what the game and other sources are telling me happened with how they want me to feel about what happened is that tone and details are being decided by two different people. More specifically, I theorize that Natsuko Ishikawa had been setting Venat up to be a villain since Shadowbringers and Yoshi P overrode it and decided he wanted her to be a hero and so they presented her that way without changing any of her actions. This is the only way I can make sense of what I'm looking at because I can't believe they'd try to sell me on Venat's actions unless someone, somewhere doesn't full get what she did.
I have considered the possibility that it's me that is misunderstanding her actions. But even if I accepted every contradictory claim made by those arguing with me. That she tried to help the Ancients, even though they have to die for her plan to handle Meteion to work. That the Ancients weren't killed, though any transformation that extreme counts at death to me. That it was the one and only possible way to save the universe...so basically, a being made by one guy couldn't possibly be defeated by anything of his species all working together? That the one and only way to save the world was for one woman to decide the fate of everyone for twelve thousand years? That's antithetical to everything in the story including Endwalker where the entire world comes together to defeat Meteion. So we could do it, cause we're superior, but they had no chance being the inferior species...seriously, I can't believe this was done on purpose...
Even if I were to accept everything at face value and hit myself in the head until I forgot about all the glaring contradictions, we end up at Gilead. A situation where it's okay to do literally anything to people if it means preserving the species...I play FF14 to relax. I want to fish and marketboard PVP without thinking about the horrors upon which this world is built. I am rooting for someone to somehow make it all make sense without my WoL being a mutated catalyst for genocide in an unending torture loop. But I mostly just get comments about the Ancients unworthiness to live or assurances their massacre was the only way cause the story says so.
Even if they retconned it and told us that we're actually volunteers that agreed to be sundered and run through her torture simulator and that the rest of the Ancients were outside of time and space waiting for us to fix the problem, I'd feel better.