There's a political conflict undercurrent within the setting of Champignon Witch, but because this is the story of Luna and how she navigates the world and her mentorship over a potential future Ruin it simply hasn't been a focus.
Back when Rudolf and Ellroy were together, the black witch hunts were ordered to stop. Though there wasn't an explicit focus, the population and the inner royal courts that cooperation with black witches and wizards began shifting to the positive as well. Some, like Elisa, probably saw the Goddess of Love giving her approval and believed that this was the right course to take. There were important figures gradually being won over to accept a new place for them in society, and with it positions of power.
That is what the orchestrators of the rebellion wanted to stop. So they carried it out, Rudolf was permanently weakened with the death of Ellroy, and the kingdom was thrown into turmoil again as Rudolf not only dealt with squashing that rebellion but also a war (or multiple) with a foreign country.
The Bird Wizard probably thought it was a safe idea for black witches and wizards to lay low after that rebellion broke out. Hence, the little progress they had made was lost while those tumultuous conflicts played out. The king who had originally ordered the hunts to stop was injured, became ill, and ultimately became unfit to rule and maintain the freeze on the hunts and they resumed. It resulted in the state of persecution that the story opened with, under Queen Helene.
Rewinding and going back to the rebellion, though. It's interesting that the war might have broken out literally right after that rebellion did.
Might this suggest that the ones responsible for the rebellion were backed by an enemy country and that was the reason for going to war?