The box, isn't evil, it's just that the Ionian Elders considers its contents "forbidden". Zed took a peak inside and saw those awesome skills, learned them and defeated his rival, then people told him "No Zed wtf that's forbidden" and sent him away.
Then he got angry and made and army, came back, got his revenge and whatever...
Zed is a Sith and Shen is a Jedi, basically. Though Zed is mostly portrayed as an evil shadow ninja supremacist and Shen as a... Neutral ninja of balance (though to this day, the lack of negative acts performed by the Kinkou makes it hard to call them entirely neutral or anything).
Same thing with Syndra really, who used to be a pretty normal person, albeit very powerful and liking it, but like they hid the forbidden ninja skills, they tried to slow her down. I cant remember exactly, but their intent was to make her evolve more slowly to avoid blowing things up hard, not to actually "seal" part of her power forever. Syndra's reaction is justified currently, as they did slow her down for years and we currently don't know of any negative effect of her rapid power growth. They could have told her but they preferred to keep silent, their loss.
So yeah, again, free will versus restrictions, which is more of a chaotic versus loyal than evil versus good.
Varus' case is... Well, he was definitely good and loyal to Ionia, following his duty until the end, but then, because of this decision, everyone he cared for died. It's unknown if it would have made a difference if he went instead of staying, but he felt powerless, and it's understandable. Then he decided to be stupid and got himself corruption all over. "I have nothing to lose so I'll take revenge anyway".
Now he's just a darkness goop corrupted symbiote bent on revenge. Kind of like Kratos in God of War, except technically more likely to become completely crazy in the end, then he'll be an evil darkness puppet. For now he's still sentient.
Now on the different case of Swain, he's evil because he's a dirty politician in a land of ruthless warriors. He makes shady deals, assassinates leaders and is more of a mage than an actual fighter. This is the kind of people Riven doesn't want in Noxus really : leaders who likely won't show up, heading their armies and fighting their all like everyone else. I don't remember his true intents though, is it ruling over Noxus and making profit/conquering others (somehow) or being a leader his nation can look up to? More of the earlier than the later really (afaik).
You know, writing this makes me think... Those Ionia champs mostly lack character development. Swain had plenty of occasions to be shady and opportunist in the JoJ, whereas Varus, Syndra and Zed are all relatively new and limited to their origin story.
I really hope we'll get more one way or another.