One word anon RETCON.
Eclipsa was not properly written but there were signs that weren't suppossed to be ignored and/or changed after S2, during S3.
The HMC was formed to deal with magic shit and was already working during Eclipsa's time, so it was obvious that they knew what she was capable of, the moment they met though is as if they had only 'heard' from her, as if they didn't live during her time and it's worse the moment the judgement begins because they make accusations based on rumors, how could they base on rumors if they fucking lived on those times. That should've been the first red light.
Glossaryck gave magic to humans and created each one of his 'children' to protect and bring balance to the use of magic. That meant wheter he likes it or not, that they had to worry about keeping the mewmans alive (specially the Queens) since they wielded magic which was, FUCKING AGAIN, given by Glossaryck himself, so how big of a douche was he to complain about his children? Why wasn't he complaining about the Queens that played with gravity, time, space, murdered half their population, etc. ?
Hekapoo apparently was tired of seeing so much death or maybe was dragged by Solaria, but during that time it's crystal clear that monster were planning to exterminate mewmans (specially Septarians), question is, why didn't Glossaryck showed up in that time and stopped it? He was magic itself with conscience, why was he such a big troll to let everything happen and pull triggers and threads all over space and time only to end with "You shouldn't have returned from magic when Toffee destroyed it Star, but at least you came to the 'logical' conclusion that magic had to be destroyed, I'm so proud."
The more you get in the story the more you understand that it was BULLSHIT. "Ohh it looks like the bad ones are these guys", "oh wait, have an episode and feel they are not, the evil one is this Dark Queen", "nope, she is a good mommy and wife". "The evil was always magic"