All data we have in game references the First Astral Era as being prehistoric, so no, it wasn't that he was so brainwashed by a dark god he imagined the people reduced to 1/14th of their intelligence as animals. It was that she turned them into animals.
And even if she hadn't devolved the species. Even if the one and only thing she did was remove their immortality, she'd still be a mass murderer. If you reduce my lifespan from 70 years to five minutes, you are a murderer.
ETA: On Ultima Thul Emet-Selch says, "My ideals are inviolate, invincible."
If he was simply tempered not only would he have not been able to take actions to end his own life, like telling the WoL where to find him after kidnapping G'raha, which his Elpis self recognized as a suicide attempt, he also wouldn't have stood there long after Zodiark was dead, say, "I regret nothing." Refuse Hydaelyn's apology by being resurrected and turn around and go right back to the aetherial sea.
Even after all is said and done, he refuses to believe the salvation of the star HAD to be bought with the blood of his people. And I believe that too. Hydaelyn was a sociopath. That is the only way she could have done half the things she did. My sense of empathy would never allow me to amass the pile of bodies she did no matter the reward.
At least Emet-Selch has the defense that what we were turned into wasn't human and he was trying to put us back together so that we were people again. Even though I'm sure that excuse got harder and harder as time passed and we re-evolved.
But Hydaelyn looked at a world of people just as human and she was and thought, "Yeah, I should kill them all and assume complete control of their world." That action passed the "morally correct" sniff test for her. And for anyone who tries to argue it was transformation, not murder, well, she knew the Ascians would kill her "transformed" children in droves and set them free to perform that duty for her. So...still the most villainous character in the FF14 universe. Thordan? Pfft, he wanted to bring an end to war, Hydaelyn wanted to make more wars. Nidhogg? He actually left Ishgard standing and gave them a chance to come over to his side. She killed all her allies. Athena? Failed Hydaelyn, get gud scrub. The Ascians. Literal pawns. They labored for 12k years in an attempt to repair what she destroyed only to discover she was just using them to up her kill count.
But hey, Answers, am I right?
ETA2: Also the Lopporrits explain that tempering was something added to the magic when the Ascians taught it to us and it's possible to create a primal without being tempered. And that with a being as powerful as Zodiark you might feel a tug. That does not sound like someone who was so brainwashed he couldn't judge people who couldn't form words anymore or became part cat to fill the gaps left in their genetic code were in need of rejoining. And Venat attempting to "stop" Zodiark's creation really isn't an act of trying to help because without informing them of the real problem, if they agreed with her and didn't summon him they would have all died in the Final Days. She needed to create discord over Zodiark so that she'd have the excuse necessary for people to sac themselves to make her a god. If she really wanted a solution besides Zodiark, she would have told them what the problem was, but she didn't. With the one and only person with knowledge of the future, she set them up to suffer and die every step of the way. People assume she tried to do good because they are assuming she's a good person and are working backwards. But her primary concern was survival and she believed the only way for her familiars to survive was if they got good at enduring suffering, which meant that every step of the way increased suffering was her goal, not decreased suffering.