Well, it's not even hard to do that for the Dark Kingdom; just portray their war as one of survival between two antithetical powers. They either wiped out the Moon Kingdom, whose power was death to them, or got wiped out by it. Of course, this is a bit of a stretch, but so is any attempt to make Sailor Moon villains come in shades of grey, really.
Don't know the R villains well enough (it's the only season I've not seen all of) so I'll skip them. The Death Busters could be portrayed as legitimately believing in a sort of Violent Buddhist philosophy where the coming of Pharoah 90 would be a legitimate blessing by cleansing all war and hatred from the world. They're also all quite insane, so that helps. Neherenia's hard, because we actually know why she did what she did and it's hard to spin it as anything other than "She was afraid of getting old, and was quite willing to eat the souls of everyone in her kingdom and kill anyone else she had to do avoid facing the fact she would age." I suppose you could make her a bit more understandable by making unaging immortality (which everyone in the Moon Kingdom seemed to have) a secret they refused to share with anyone else.
Galaxia's easy, and actually my favourite pet theory about the anime (though it draws some inspiration from the manga). She fought the war against evil for uncountable years. She threw down a hundred Dark Kingdoms, Black Moons, and false Messiahs, and saw a thousand more rise in their place. They all stemmed from the same force: Chaos. It was a never-ending war that even the greatest soldier of all could never win. So, unable to bear that, she took the fight to Chaos itself. She fought the very concept of evil and hatred, and
she won (because anime Galaxia is awesome like that). But though she could defeat Chaos, defeat even the very concept of war, she could not destroy it - and tragically, the perfect warrior's only flaw was hubris. Unwilling to admit defeat even then, she sealed Chaos within herself. If she could beat it, surely she could contain it. Of course, she knew immediately her mistake - all she had done was give Chaos, which could not strike her down openly, the vulnerability it needed to corrupt her from inside. That battle, she could not win. Hence, the series. But, for a time, all evil was sealed away. For a time, kingdoms that knew only peace and love flourished, because the very concept of evil and conflict had been locked away by an unknown saviour. For a thousand years, a glittering kingdom on the moon of the third planet in an otherwise unremarkable solar system enjoyed the peace and prosperity that Galaxia's sacrifice had brought. Without her, nothing like it could ever have existed.