Hooboy I had a lot of things to write. Sorry about that sir or madam.
History is not solely determined by the victors. There have been many losers throughout history that survived to write about their enemies and there have been many on the victorious side to write about their foes. Few victors go on to completely eliminate those they defeated. Often times they will assimilate or be assimilated into the conquered (The Mongols are a good example). We know lot about civilizations that were destroyed from their own records and what they left behind and what the destroyers recorded as well (The Aztecs for example). It's easy to try and doubt history by saying 'It's only written by the victors' when it's far more nuanced than that.
I agree that evil is a label. I personally think no one in real life and few good fictional characters actually think what they do is evil. One could argue there are no evil people, just evil actions. But that doesn't excuse those actions.
Different time periods have different morals yes, but we can only look at things through the morals of today. We can say slave holders were not racist by the standards of their time, but that doesn't excuse their actions. Noxian actions like the chemical warfare and genocide of the minotaurs are still wrong regardless of what they thought or were taught. Moral relativism is a dangerous path I think.
There are commonalities of what is moral throughout cultures. Murder as 'unjustified killing,' theft as 'unjustified taking' and such. Even though what is justified can vary there is growing consensus on what is moral and what is not. Cannibalism is pretty much agreed on to be immoral now except in dire circumstances for example. Slavery is legal or accepted in a few places but is getting cracked down on. Human sacrifice is a no no. Beating children or spouses is becoming less acceptable.
Noxus and maybe Zaun and parts of Bilgewater seem to be the exceptions to RuneTerran morals (I'm excluding nonhuman sides like the Trolls, Void, and Shadow Isles for simplicity). I could be wrong but it seems no one else but Noxus and Zaun and maybe Bilgewater are okay with chemical warfare, killing your way up the social ladder, genocide and other 'atrocities.' Bilgewater might be okay with killing to advance personal goals (like father like son), but I don't think even Gangplank would kill every member of a ethnic group or species or use horrific chemicals against his enemies (unless you count grog soaked blade, man than can get annoying).
Noxus was pretty much meant to be the dark and Demacia the light by Riot. Looking at their art styles, champion motivations and quotes and their philosophies, it's hard to argue that Noxus is actually good or not as bad as Demacia. I see a lot of people claim that Noxus is better than Demacia because of the meritocratic nature of things and Demacian laws. While this can be true I don't think any of us would survive long there as I don't think any of us is prepared to kill (at least I hope not). What we see of Noxian meritocracy is rule by the strong and ruthless, not something we in the real world in general like to think as a good way to govern. The city is built in the shape of a skull too...not very subtle. To me those who see Noxus as better because of the meritocracy overestimate how well they'd do in Noxus.
Demacia has far fewer negative tropes associated with it. Off the top of my head I can only really think of the Lux being forced into the military, a remark by Caitlin on their strict laws and maybe a bit with Quinn being exceptional as a commoner rising into the ranks. I'm likely missing some, but overall Demacia comes out better in what it has done or hasn't done. A monarchy isn't necessarily a bad thing if the monarch is wise and just. A social ladder that can be climbed with great effort, is better than one in which the way to climb is to knife each other.
So pretty much Noxus need to be written more subtly I think to be an equal moral alternative to Demacia. Cut back on the genocide and bloodlust and necromancy (keep Sion though) and promotion-via-murder and maybe some urban planning to remove the skull. I'd like Demacia and Noxus to be two powerful city states with opposing but viable societies. One where laws are strict but just and one where laws are lax but the rewards greater. One with a sense of honor based on unwieldy codes of conduct, one with honor based on defeating your enemy without causing undo suffering.
Pretty much the same for Piltover and Zaun as well I suppose. Neither has to be 'evil' in their actions , but you can still make them morally equivalent rivals.