The argument isn't that the Ancients were perfect so much as they didn't deserve to have some deluded nutter waltz in, inflict genocide upon them, declare herself to be a 'supreme deity' and then try to stifle all memory of their existence.

I don't care about the 'moral' stuff, it's a video game at the end of the day. Not the real world. I just like and desire consistency. If a game's story is going to fill my screen with lengthy sophistry fuelled rants from characters that are given every possible advantage in order to succeed then I'd rather not see the game apply its supposed 'rules' across the board and not hide the actual consequences of the likes of the Sundering behind feel good, fluffy language.