Quick note: The Mursaat and the Stone SUmmit in THK will attack each other. This is most easily seen if you do the Bonus and refrain from killing anything.
On Relativism, just cuz the Pope said relativism is evil, doesn't mean it is. The Pope also equated Led Zepplin, ACDC, and the Eagles. Clearly this is nonsense as the Eagles don't hold a candle to ACDC and Led Zepplin.
On intentional evil, I disagree with QA that some people want to do bad things. Since I don't want to get into a "thing" here I'll just say I pretty much agree with Socrates' arguments in Plato's "Meno" dialouge.
Are the mursaat evil? No.
Consider this. We, the players, are the Chosen referred to by the Flameseeker Prophecies. The Mursaat have been keeping the door closed for at least 2 years when we begin in Ascalon, but probably more. Now, if the Mursaat HADN'T been keeping the door closed by slaughtering innocents, the Titans would have been released BEFORE the players were there to stop them destroying the entire world.
So we see the Mursaat were preventing the Apocalypse through somewhat distasteful means.
Consider this. The Flameseeker Prophecies also said the opening of the door would destroy all of the Mursaat. Now, it is unlikely that the entire Mursaat race is currently at war, they must have a civilian population somewhere (this isn't Robotech after all). So if they hadn't kept the door closed and somehow the titans manage to not negate all existance, they would still have murdered every Mursaat civilian.
Finally, consider this. The Flameseeker Prophecies take a very Greek idea of Naive Fatalism towards future events. Namely that some important things are inevitable but the details can be fudged. E.G. greek mythology see Oedipus. In this context, the Mursaat didn't EVEN HAVE A CHOICE. They were as much bound by fate as we were to open the door. Even if they had wanted to, they couldn't have not guarded that door and kept it closed. In fact, they couldn't even have not wanted to. Leibniz has a good example of this kind of Determinism in his "Discourse on Metaphysics"