Just a correction: they aren't "light" ninjas.
They're ninjas of the Kinkou Order.
The core aspect of the Kinkou Order is their undying faith in the concept of balance.
This means that the Kinkou order ensures there is a balance between good and evil. Order and chaos.
Because that's the way they think the universe was meant to be. Neither in harmony, nor in discord.
This means that they aren't "light" ninjas. They use a combination of both light and dark magic in order to uphold balance.
Take Shen for example. What is his E called? Shadow Dash.
What about Akali? What is her ult called? Shadow Dance. What is her Passive called? Twin disciplines.
Not to mention Shen's Twillight Assault and Akali's Twillight Shroud.
This is taken from the Wikipedia:
"Twilight on Earth is the illumination of the lower atmosphere when the Sun itself is not directly visible because it is below the horizon. Twilight is produced by sunlight scattering in the upper atmosphere, illuminating the lower atmosphere so that Earth's surface is neither completely lit nor completely dark."
As you can see, the Twillight in the names of their abilities suggest they meld light and shadow magic together in perfect balance.
Thus, they clearly aren't "light" ninjas (Kennen is the one exception considering he almost exclusively uses lightning magic).
The only thing that doesn't add up is the fact that even though they use Shadow magic themselves, they openly oppose Zed's Order of Shadows and their use of shadow magic.
I'm guessing this is because Zed uses Shadow magic exclusively, whilst someone like Shen tries to uphold balance by using light magic to supplement.
And neither of them are "correct". I'd say Shen and Zed are both morally gray in their actions.
Yes, Shen sounds like a "good" guy because he protects people, but in his short story (titled True Neutral just like the alignment in D&D) he is also shown to kill other people, even an Ionian priest, in order to "uphold" balance.
Likewise, Zed sounds like a "bad" guy because his Shadow Order wants to kill all other ninjas that refuse to learn his techniques, but Zed's actions might be justified.
After his master, Lord Kusho, spared Khada Jhin, he felt betrayed on a personal level. This is what led him to opening the box in the temple and ended in Lord Kusho's death, the fall of the Kinkou Order and the rise of his new Shadow Order.
He could have his reasons to do this. He might think Lord Kusho is no longer capable of carrying out the task of being the "Eye of Twillight" since he spared Jhin.
He might have killed the other Kinkou ninjas because in his eyes they've all been manipulated under Lord Kusho's guidance and they're beyond redemption.
Perhaps he simply thinks that the "old ways" of believing in balance has come to an end and in order to fully harness one's potential, all must embrace the shadow and eliminate those who refuse to conform. This is why Zed doesn't put any restrictions on his students because in his eyes, restraint only leads to weakness. Just like how Lord Kusho restrained from killing Jhin and thus Zed perceives him as "weak".
It could also be because of the box in the temple that he opened. It might have corrupted, and could quite possibly even have possessed him and it's not even the "real" Zed that's in control.
Whatever the case, it's not really fair to just flat out call Zed "evil" because he's not. Yes, he might do some morally ambiguous things but in his eyes, what he does is the right thing to do.
Hell, he even set aside his differences with Shen and his Kinkou Order to sign a truce with them in order to deal with the newly released Jhin.
If that sounds evil to you, I've clearly failed in my explanation.