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These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Fujimaru is initially one of these, before dropping the Jerkass part and moving into general Woobie territory. Eventually, he graduates into an Iron Woobie.
Amagiya towards the end of the series, as his backstory is revealed.
Magnificent Bitch: Kuroyuki is utterly despicable, but you have to give kudos to her for being composed and competent through it all.
Moe: Shirayuki is generally agreed to be the cutest thing ever.
Moral Event Horizon: You could argue when exactly Kuroyuki crossed this, but she definitely has at some point.
Chronologically, experimenting on her own daughter pre-series is this.
In terms of the present, however, her telling Takeru to roll over and give up makes it clear that she knows that she's no saviour. It's also the moment where Takeru decides that she has to be taken down, and his will never wavers from there.