Vader and the Emperor both seem to really revel in saying "the Dark Side" with emphasis, as well as doing and inspiring "dark deeds", so I think they would say that in their own histories, too.
But let's see... if we assume that not only is there a victor filter, but also an Earth English filter from the writer/inventor Lucas, and we pretend that Lucas is making an Earth-accessible version of a Light-Side-biased history, and the film versions are unfair demonizing caricatures... that opens more possibilities, but also means we need to provide our own guesses about their actual nature, and then find our own ways to convey those in this language which is so full of dark/light moral connotations of our own.
I think though that it seems like Dark Side philosophy seems to be unashamedly that anger, rage, revenge, destruction, violence, threats, terror, brutality, torment, torture, and selfishness are all good, fine and dandy. I don't think the darkness connotations will be the only issues. To try to be "politically correct" or at least neutral, one could say "the Lightless Side" or "the Dim Side" or "the Black Side", but I think that would miss their point. They like being the Dark Side, and want you to be terrified and think of them as murderous horrible hateful despotic loathsome torturing despotic overlords.
Only if we decide that Light Side propagandists made all of THAT up too, and that the Dark Side folks were actually misunderstood, with equally reasonable philosophical alternatives, then maybe it might make sense to look for less loaded terms. Maybe the Sith just wanted to be allowed to play with light sabers and use the force and ALSO have girlfriends (dumb emotion-stifling Jedi rules be damned!), and to keep their dying girlfriends alive, and maybe they had great ideas for economic development, great military service benefits, abundant gun rights, great advances in GMO soldier-cloning technology, and the Death Star could also be used as a giant holographic sky-wide movie projector to entertain the masses and so on.
Maybe they were the Black Side, or even the Indigo Side or the Colorful Side, the Deep Side, the Dusk Side, and/or the Night Side.
Or maybe the whole dark/light thing was a Light-side propaganda point, and they really just called themselves the Sith, or the Cathartic Side, but that doesn't really get at the question of what English words for dark don't have negative connotations.
I'd say the negative connotations with "dark" goes beyond words, to the ancient metaphor of the underworld as a dark world beneath where there is death and darkness. You can find words people aren't used to hearing, and use say, the Atramentous Side, which might be my best shot, but the metaphor about darkness itself may still be there, for Earthlings.
I suppose "the Shady Side" has positive connotations even if it also has dark ones.
Best Answer
A stimulus that is below the threshold of conscious perception, but nevertheless influences one’s mental processes is said to be subliminal, or to influence them subliminally. As the OP requested, characterising some influence on a person as subliminal, does not imply anything as to whether the influence, or the motivation for it, is good, bad, or neutral. The Wikipedia article on the topic provides a serviceable explanation of the concept. The term started out as a technical term of psychology, but quite a few people have by now heard at least some popular outline of this phenomenon to be able to understand the term. In informal speaking and writing, the term is often used more loosely than among professional psychologists.