I don't think anyone's problem with the ancients is that create things that they then destroy. I mean - Hermes does, but even his issues with their society go deeper than that. It's more that these beings were created to follow trends and were then discarded when they were deemed no longer useful. When it comes to the examples you gave, those all have a practical utility, born of out necessity. (also, is summoning and unsummoning a familiar/egi even the same as unmaking a creation? Unmaking seems like a pretty distinct and final destruction of a concept. When Mataoya unsummons her poroggo, she can summon more later, even the same poroggo as before, since they seem to remember previous instructions or interactions with you. When the lykaones were unmade, it seemed to be implied that nobody could ever create one again.)
Also, I think you're conflating moral superiority with physical superiority. I'm not superior to someone who is immunocompromized just because they could die from the flu. All anyone has pointed out is that like any culture, they have their flaws and blind spots. And that fact alone pokes a giant hole in Emet-Selch's view that everything was perfect before the sundering, or that there is no point in life that came after because that life is flawed.
Edit: Emet-Selch is presented as a villain to be slain because he puts himself in that role. He opposes you trying to prevent the flooding of the first with light, and the rejoining. He talks with you, he tries to reason with you, but you are a hero, and refuse to step aside so that everyone you love on the first can be killed in a rejoining. With neither of you willing to budge on your positions, conflict is inevitable. Even then, Emet-Selch is presented as tragic and sympathetic. And by the time of Endwalker, he isn't presented as a villain at all.
