@thomasce
They already established that humanity was suppose to follow the witches originally. If his goal is to have singular power over humanity, makes sense being the emperor of mankind, then that alone is reason enough to kill them all once he doesn't need them. Having developed technology that surpassed them isn't the reason to kill them, it eliminated the reason he had for keeping them around. As for society as a whole, you saw with his speech. He's rallying them into this, playing on fears and making up (or not, who knows. her reaction of threatening the people to protect the mc wouldn't need to be spun negatively for the people present.) slights against humanity.
I mean, dude, you don't even have to go into history like YukiOnna did. We have enough examples of this TODAY. One of the US's biggest allied dictatorships (US is allied to about 70% of the worlds dictators) just had a big thing where they started letting women drive to show that they are "improving and civilized" but executed all the women who were protesting for the right afterwards. All of that is because protesters are a challenge to their authority.