Very good question. I will give you my thoughts on each of the factions you mentioned:
Scourge: I have sympathy for this faction because some many did not have a choice, remember some were created via the plague and others were raised from the dead. The scourge in The Maw are created from tortured Kyrian in some cases, so these are beings forced to do evil.
Necrolords (SL Covenant): As defenders of SL, I would say their actions are pretty justified they are protecting the SL and meant to be a line of defense, they are the warriors of the Shadowlands. I would say their actions are justified.
Necrolords (Creators of Scourge): no sympathy here as they are raising the undead to be members of the scourge. Not sure how anyone can justify their actions.
Kyrian: I do not agree with their method of wiping ones memories clean but they are considered the purest souls in the SL, so while I agree with thier mission, I do not agree with wiping memories, we see that this can lead to nightmares and corruption as it did to Uther.
Scarlet Crusade: I agree with their methods of purging the scourge but not with their beliefs about the alliance and their being against working with the horde. I think they are simply trying to further their own aims and cause dissension.
The moral difference? Easy, the Scourge was mind controlled, the Necrolords just recruit psychopaths. Yes, characters like Emeni are about as evil as it gets.
That’s actually what I appreciate about the Necrolords. Once again we have a faction that doesn’t make everything about modern morality. There might be some morally upstanding warriors among them, like Morgraine, but as a whole that lot is entirely amoral.
I can play there without being hit over the head with the obvious message that violence is bad, hmkay?
Having switched to Necrolords in 9.1 both out of spite and for something new (Seriously, Kyrian just because I love tanking? eugh), Alexandros Morgraine goes through this during the covenant quest in which Maldraxxus starts paying reparations for what the Houses of Rituals and Constructs did to Bastion.
Overall, there isn’t really anything moral about them. At least in the way we look at it. They are built on a simple code that is sacrosanct to their purpose and being, which is to protect the Shadowlands and be its most powerful standing army.
So it seems in order to do that, souls of great and powerful might are called to it to live out an existence of eternal battle. Which evidently from some NPC’s is considered a dream come true, so long as they answer the call. It seems that if you don’t, or do something else that stands apart from its ideal, it is a very quick way of getting yourself killed.
It’s really a play by the rules thing. You serve by doing what you loved doing, or what represented you best in life: Your ability to fight and strive in the heat of battlefields and wars.