Gonna have to explain more on why humans as a whole all of a sudden hate witches. One or two people is easy enough to swallow, and maybe a small group is reasonable enough. But for an entire population to turn on witches that have apparently been helping them the entire time makes little sense without some sort of major driving force. Whether or not I follow this or not will depend entirely on whether they explain this potential plot hole well enough, because hand waving isn't enough for me in this case.
Chloe's only reason to not massacre a square filled with civilians and why she allowed the citizens of a nation to live is only because her apprentice is human. Surely the humans should be very gracious and thankful that they are allowed to live.
Chloe thinking "Even thouh I've let you live until now" when reffering to a WHOLE nation is just insane. Like seriously, Chloe contemplated genociding a whole nation, and she is framing it like she did humans a favor for not doing it until now.
Assuming Chloe mentality is not uncommen, human fear and hate for witches are completly founded.