I think that Eclipsa will indeed be evil in the end, or at least dangerously amoral, but it'll be a slight twist.
At first, Nefcy will lead us (and Star, probably) to believe that she's a victim of blackpainting and anti-monster propaganda because she ran off with a monster, that she's not really all that bad, and will connect with Star and seem like the cool vodka aunt, a mentor-like figure.
But eventually it'll turn out that yeah, her main interests in magic being the dark arts and dabbling with ancient evil forces, her chapter being full of dark evil shit, eternal suffering and so on so badly that it had to be locked, and her having become so threatening that Rhombulus had to encase her in crystal were all indicative of something, and in the end she is indeed the main antagonist, who'll almost succeed in corrupting Star and converting her into her own worldview.
I mean she dabbled with the dark arts and invented new sinister spells. Apparently she's also made a deal with something horrific that was corrupting her, which she then managed to shift off to Moon. I wouldn't be surprised if it turned out she's been developing the spells via experimenting on mewmen or some shit like that, it takes some trial and error to come up with new spells, I'd guess.