They did a shoddy job of writing Hydaelyn as a heroine. Even her staunchest supporters agree that if the sundering wasn't necessary then it's morally unjustifiable and the narrative no longer works. The problem is they left the door wide open to doubt that the sundering was necessary. Not only that, even if it were 100% guaranteed that the Ancients would eventually 'be their own undoing' that still in no way makes genocide an acceptable response. "I'll destroy you before you can destroy yourselves" is absolutely stupid.

Just because Hydaelyn "helps" the WoL doesn't make her not an antagonist either, especially considering she'd put all her eggs in the WoL's basket so it's in her own self interest to assure that her 'chosen champion' survives to carry out her will. However, objectively speaking from a world history POV, she is without question one of the two primary antagonists second only to Hermes.