Wouldn't this kind of idea just justify Moondancer's arc completely?  Moony was a villain, but now it has come to a full circle as he now takes the role that usually female characters take in some movies: The member of an often ignored or overlooked minority, with family troubles, trying to prove himself better to a society and trying to bring down an all powerful monster (Pandora). 



We see that most magicians have been female, and they are now mostly female, hence there should be a kind of repression towards males and a tacit thought of "magic is not for males", maybe not expressed openly, but known by all.  The only magic user that is male is Discord, and Discord is a god of Chaos, not someone who learned magic as such.  So we have a member of a minority: White male (I know that pelt color is picked at random, but really, Moony couldn't be whiter if he tried xD), heterosexual, not willing to explore sexuality with males (in this verse), trying to win a talent usually aimed to those of the other gender, denied by his father, lied to by his mother, denied by his friends, ignored most of his life.  In my humble opinion, the more we dig into the backstory the more Moony is starting to be justified about his ambition and want for power, because his search is starting to become exactly like the usual searches of most heroes.  He's shifting the power from one majority to his minority, heck, seen with the theory of Otherness his quest is even inspiring as he's been working hard and doing sacrifices to be where he is now, and is still going, attacking a society that is starting to be proven as hypocritical. 



While Pandora is a monster, but it's not a conflicted monster, she's open about her looks and her powers, even when she has scared others with said powers, even when her plans backfire and she scars the society she's in once and over she's not trying to separate herself for a "greater good" nor is she trying to find a way to remove her powers that have damaged those around her, instead she uses them for her own benefit and amusement.  That's pretty much the definition of a villain. 



Even when Moony has been shown to be this near heartless character he has started making a change in society, as with his powers he'd defeat one or two monsters (Pandora and/or Discord) and return a somehow normal life to the equestrian society, now taking a place of "the strongest" and hence the "protector", which we know he'll keep as it's his goal.  Pandora has no other goal than mayhem and chaos and when she has it backfires more often than not, Moony is a controlled danger, Pandora is a wild card that could destroy the whole society if she so wished. 



I think we're starting to arrive to a "Moony is the good guy" conclusion due to the extended backstories.