"Friendship is magic. . . and so is Hatred."
There is already chaos magic that is the antithesis of the magic of Harmony, but how about Hatred, the antithesis of Friendship, being a magical force just like it.
As in the opposite/antithesis of Friendship existing in the world as an actual force of equal power as Friendship. Both as Magic and as an Emotion.
It would be this magical force that the Villains and negative creatures are either spawned from or derived their powers from. Windigoes being a manifestation of the Magic of Hatred. The evil forms of alicorns being the result of them being corrupted by the magic of hatred. Sombra's dark magic and his Umbrum kin being derived from Hatred itself. Chrysalis trying so desperately to stay evil and reject any form of friendship and redemption because she found comfort and safety for her kind in the magic of Hatred. The magic of Hatred being what made Tirek so power-hungry as it consumed him and made him addicted to it. The Thracian Ponies being ponies that rejected Friendship and embraced the Magic of Hatred. The Sirens being described as the "voice/mouthpiece of the magic of Hatred".etc.
Even the creation of the "mean six" by Chrysalis and Discord would involve them drawing from the Magic of Hatred itself to create them.
There could also be something where instead of being a fragment of the tree of harmony, the Storm King's Staff of Sacanas is instead one of many tools used to harness the magic of hatred.
There'd also be this thing where Hatred and and Friendship as a magical forces have always together, side-to-side, and that they have been locked in an eternal conflict since time immemorial. No matter how hard the wielders of Friendship and Hatred try to wipe each other out, as both forces are of equal power, they are never truly able to completely wipe out one another and they continue to persist and will simply go dormant if all the users of that magic are completely exterminated. Waiting for the day that new wielders worthy of either powers come into existence and reawaken both powers.
However, those that wield or embrace the magic of hatred don't usually last long. It eventually consumes them and ravages them physically and mentally and eventually becomes their undoing. Although being of equal power, Hatred, like in real life, would lead those who express or wield it to go down a self destructive path in which their destructive behaviors ravages their own physical and mental wellbeing. And this is why the Villains of the legion of Doom are so irrational and would not be able to properly cooperate with one another. Friendship helps people and brings them together. Hatred divides people and eventually destroys them.
This would also be an alternate justification as to why these villains reject and despise Friendship. They were seduced by the intoxicating power of Hatred. It gave them great and terrible power but they don't realize that it'll be at the cost of their physical or mental health as spiral into a bottomless pit of self destruction.
That's just my two-cents. How do you think Hasbro and the Show's writers would have depicted the "Magic of Hatred"?
These were a "lost tribe": of Ponies that wanted to invade Equestria and commit genocide against ponykind as revenge for the other three tribes not wanting to share the fire of Friendship with them. Lijke all other villains, viewing Friendship as weakness. For this idea, their rejection and resentment of Friendship would be because they embracing the magic of hatred. F Friendship is weakness, Hatred is strength!