Okay, you say that, but as of the current show, she really didn't do anything.>Toffee dies, Queen contract is satisfied and she's set free>Gets immediately locked up>Helps Moon figure out the mystery behind the Butterfly lineage>Helps Moon track down Meteora to try and stop her carnage>Successfully defeats Meteora
After that, she tries her best to be a fair queen and make changes that benefit monsters (given how unfairly they've been treated before). The most wrong she's done is attack, then body-swap Rhombulus, but the former is because it was mainly self-defense, and the latter because she just wanted to be with her love. She acknowledged that what she did was wrong.
As for what happened before the events of the show, no one can be certain. The worst thing she did was "abandon" her kingdom to run off with "a monster". Since Mewni is more or less a matriarchy, having the queen run away isn't exactly the best, but who could blame her? She was forced to marry someone she didn't love simply because it was politically beneficial, then he was attempting to force her to bear his children. As for the dark magic, it hasn't been explicitly stated that she used her magic to hurt or harm. If the sole reason that one's arms turn black is when they use the killing spell, then it could possibly be assumed that she may have nuked a couple of folks. If there're more spells that turn the arms black, then she may not have killed anyone, and she just had to bear that side effects of using dark magic.
It's hard to take any accusations against her seriously, given the reputation that the MHC has established for themselves. If they didn't interfere with Eclipsa and her family, Meteora wouldn't have grown up to rampage the kingdom. Almost all of the negativity directed at Eclipsa is little more than prejudices.