Honestly I think they where going with Magic=Privilege , what with the first Mewman being given the wand by chance and the artificial nature of it being shown how easily Eclipsa and Butterfly family where swapped in and out.
But that gets totally undermined by the fact that they introduced all these magical beings who exist because of it.
When power changes hands in real life no one just drops dead as a direct result.
Maybe they where trying to portray the MHC as metaphor's for the structures that hold up unjust hierarchies, whose existance is justified by said purpose.
However they've clearly been established as autonomous beings.
I think they where trying to go for a progressive message but just ended up with "sometimes a whole group needs to be exterminated for the betterment of society".