I like to think that, were Seija to succeed, she'd eventually

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I like to think that, were Seija to succeed, she'd eventually start opposing the very new reign she created and keep doing it ad nauseum until she failed. The thing is that following one's nature must take into account to what point it affects them.
Animals are slaves to their nature, we don't consider a tiger evil for hunting its prey, nor a dog good because it licks it owner.
As far as humans go (ignore some philosophers since that's not the sort of discussion we ought to be having) they're free to go against their nature. In fact, everything we do that is considered good or evil are the acts that go against one's instincts beyond survival and propagation.
Now comes Amanojaku, and you could extend this to Youkai. The biggest problem is that we just can't understand a point of view of a being whose nature is to go against things(I'm borrowing some dude's idea here, but most other sentient things in fiction barely ever go beyond human attitude with a small twist, things beyond our comprehension are left in the dark, like lovecratian gods), I mean, there's no sentinence we can understand beyond our own, so the question as to whether Seija is evil or not, is how strong the Amanojaku nature is, if it's too strong, you'd then argue that her neutral actions are what she did, and to be evil or good would be her geing against her Amanojaku nature. If it's too weak, then it's the opposite, the path she takes is her being too weak-willed to go against her Amanojaku blood and succumbing to it.
To sum it up, I mean to say you can't pinpoint her morality unless you knew how her youkai type works, which we'll never be able to because we can only understand how it's like to be human.