A campaign I ran a few years ago involvled a lot of issues about morality, good, evil and all the sorts of things this thread is talking about. This is sort of relevant to the idea of two groups both considering themselves good.
I should point out that this was a Rolemaster campaing, without alignments; but there was still a very clear distinction between good and evil as embodied in the gods and general religious beliefs following on from their attitudes.
The campaign ended up with fairly strong religious themes; about half the party used magic that would in d&d terms be considered divine (or partially divine).
Once the overriding plot had established itself, it was a fairly typical "We are the good guys, serving some nice gods, seeking to prevent the return of a long banished god of ultimate evil."
As the campaign progressed, it became clear that some gods (most of them evil) seemed to be dying. The followers of a some of these gods had turned to a new cult prophesying the coming of a new power. The party began to learn that a mega-powerful seafaring race were in fact long-fallen gods of another pantheon that once coexisted with the currently worshipped gods. And they met a rather nasty fellow who had worshipped a vicious, xenophobic, human sacrificing god of a foreign pantheon. This PC quickly learned that his god too was dead, and that another had stepped in to take his place. This new god was one known to the rest of the party, and was also evil. But this evil god was telling his cleric to work with the good guys. And the good guys' gods were saying let him.
Finally, towards the very end of the campaign, the Demon Lord Sith, one of the highest servants of the enemy, appeared to the group and told his side of the story.
Big Nasty Coming Back from the Dead god was at war with most of the other gods. A few had come over to his side. It was admitted openly that he was not a nice guy. But, he had a genuine problem with the way the current set of gods treated the PCs world. He saw the rest of the gods as a bunch of silly, bickering children who used the races of this world to fight their endless wars. He pointed out how fickle they were, and how easily they suddenly joined forces with sworn enemies at opposite ends of the moral spectrum, to fight him. How they would return straight to their infighting, if they won. And how the people of the world would continue to be no more than pawns in their endless game.
He explained how both he and the previously mentioned race of fallen gods had been cast down because they didn't agree with all this foolishness.
He had returned for revenge, yes, but if he got it, he would not make the world a terrible place. He would leave it in peace - he had better things to do than torment a few mortals for sick pleasure. Unlike the current regime.
In the end, the party split down the middle, half of them going over to the "bad" guys, the other half staying with the "good" guys. (Except one PC, who commited suicide because she believed changing sides was morally wrong, but the PC she loved had gone over).
The most enjoyable aspect for me was that the two groups, unknowingly, virtually proved Sith's point for him.
The "good" guys hated their betraying friends, and wanted them to suffer an eternity of pain for their actions.
The "bad" guys hated having had to betray their friends, and wanted the final showdown to be as bloodless as possible.
Anyway, possibly some ideas in there for anyone wanted to run a campaign with blurred moral and ethical lines.
Oh yeah, the "bad" guys won. And the world ended up being a much better place for it. (If the "good" guys had triumphed, the world would also have ended up being better for it (it was pretty screwed at the start of the campaign, with evil gods prevailing overall), but the new stability would have fallen appart after a few millenia, at most.)
) demonstrates that aspect well.
