There's no way she won't be treated as a villain by everyone in the greater setting. The Magic High Commission almost shit themselves just because Star was reading her notes unsupervised.
That said, she is in a unique position where most of the characters we're actually focusing on probably wouldn't treat her as a villain outright, on their own judgement. Star clearly doesn't take her seriously and seems to even admire her a little, Marco is a human who would probably defer to however Star ends up dealing with her (though more cautiously, considering he was actually possessed), Ludo is almost certainly ignorant of her entirely, Buff Frog probably is too but between his competence and his good relationship with Star probably wouldn't go picking a fight with a Butterfly Queen.
Moon isn't prejudiced against monsters and seems aware that the "monster love" thing has demonized Eclipsa to some extent, and her reactions to Star meddling with Eclipsa have been more restrained than the MHC's or River's, though she's still clearly concerned. She would oppose Eclipsa more on the basis of her being a legitimate threat to the Kingdom and Star's wellbeing than whether or not Eclipsa was/is a bad person. Not even getting into the fact that the thing Moon apparently made a pact with for her "Darkest Spell" was probably Eclipsa.
As for Toffee, we just don't know enough about either to do anything but speculate.
In my opinion,
1. Eclipsa definitely isn't all bad. She has way too many sympathy flags, between her clear parallels with Star and running away with her true love. We already have a straight BBEG villain in Toffee.
2. Eclipsa is still pretty bad.
3. The Eclipsa/Toffee connection is a red herring.
4. Eclipsa's role in the story will be a third/fourth party, not aligned to the Mewmans or Toffee's monsters. She will want peace between Mewmans and Monsters, on her own terms, by force if necessary. She will fight both sides while trying to get Star on her own.