Well, maybe we should take a step away from the theoretical thinking - because if we prove that there ain't no good or evil, no black and white, then I will stop to bother if I need to switch on my headlights in the evening.
Can we collect some facts? I'm not the canon specialist (sublime call going out to Loaf, Chris, Hades... - anyone not mentioned please call my lawyer), but maybe we can shed some light into the conundrum if we analyze the fictional facts.
Human culture in the 27th century is, more or less, based on what we have - and given that WC rather builds on a Western culture, it goes down to the moral concepts laid down in something like the 10 commandments: Don't kill, don't cheat, don't steal, don't bulldoze your way over others, respect your elders, and try to solve conflicts without violence. Everything above that is considered "bad", although necessary under certain circumstances (war), but even then there is still the personal conscience to overcome (take Archer in WCA).
Kilrathi culture (and here I start to walk out onto thin ice) cis based on the teachings of Sivar, so there's also a spiritual/cultural base to it. But Sivar teaches different things: Personal success is above everything, and the means are violence, cheating, killing anyone who's in the way, dominating anyone who is clever enough to submit. In addition, there is the clan system that regulates civil war breaking out all the time. Compassion, surrender, mercy etc. are regarded as weak, and therefore as "bad" - and there are no general circumstances that allow to go that path of action. But for personal decisions, it seems the other way round - and I'd like to take Hobbes as an example. He turned away from the action of his people because his personal interpretation regarded them as "bad", but he turned back to them when his homeworld was in danger, because his personal morals now regarded the humans, and even his best friend, as "bad".
And I won't say much about the Nephilim, because I don't know anything. Just somewhere earlier in this thread, somebody said that the humans are the only culture we know of to have built complex social structures; and I thought, 'well, disregarding insectoid cultures, it's true'. Here we have an insectoid culture - whose value systems we can only guess at.
So, who's bad? My personal value system would point towards the Kilrathi and Nephilim, because their actions are "bad" in my eyes.
But what is the WC Universe telling me then? There are evil forces afoot, and you'll need to be prepared to react anytime, strike back at the first aggression, stick only to people I know and suspect everybody else? Hmm, my little moral guidance system says, I can see some Kilrathi traits in there...
But maybe these facts all got jumbled in my mind and somebody can help me figure them out. And again: I'm not trying to be a cultural relativist, whatever negative connotation this may carry at the moment.