The Ancients didn't deserve it, but it's not as though Venat and Hermes were outside forces either. They didn't just "waltz in". They were both Ancients and products of the society in different ways. Venat's adventuring gave her a different point of view from the rest of her society and it's likely Azem was the same, even if she did not reach the same conclusions. But they both chaffed at the norms and questioned the heart of their culture. Hermes cared too much in an apathetic world and then went crazy after his creations that he programmed poorly gave him news he didn't want to hear and decided that he should test the world and end it all. Hopefully we get some sort of Tales from the Dawn or something that will go deeper into their reasons why they did what they did. There's no doubt that we'll have one from Venat's point of view.
I don't recall Hydaelyn referring to herself as a "supreme deity" but the Ascians sure had things to say about their own Dark Lord and Savior, Zodiark and about how great He is and how he will plunge the world into Darkness.
You haven't been paying attention to anything at all then.
Ancient Concepts/Creation magic - Can be anything from clothing, to cities, to creatures.
Concepts at Elpis - Flesh and blood creatures designed to become part of the ecosystem and even perhaps gain souls and become an integral part of the Lifestream and the circle of life. When these die in Elpis, they still remain as corpses as normal animals would.
Familiars - Both in the Ancient and modern days, beings created of pure aether and can be dismissed into aether. They are created for a specific task.
The heart at the debate is whether Y'shtola sending nixies into the Void is comparable to the Ancients' treatment of their concepts at Elpis and I say "no" because they're two different things. Familiars are not alive in the same way. They have a task embedded into their existence that shapes their entire reason for being. They do not have real bodies either. Nixies are water, porxies are clay (as one amaro found out when attempting to eat one), and carbuncles are a matrix of aether around a stone. A sidequest in Elpis even mentions that they're usually "fed" aether, not real food. Y'shtola's nixies don't even die, she dismisses them as one would dismiss a carbuncle.