Regardless of the damage, I'd say no one person can be purely good or purely evil whether they intend it or not. The interesting play on justice comes when she either decrees this happened for the greater good, or other people condemn her as pure evil when it's an act that she now regrets. It'd probably be most interesting if the civilisation around her declares it justice (which I can see happening with your emperor figure) but she has to struggle to fix her wrongs in world where everyone believes they were right in the first place.
(I'm just speculating now, I need to read this instead hahaa)
(also i absolutely love your art, the pale colours with those strong red backgrounds look so cool)