First, Ninja School is kill-or-be-killed. That guy knew the score when he enrolled and probably did it to the guy ahead of him.
Second, I'm more concerned with her activity in the comic than an implied history that I haven't bothered to work out. Kubota was teaching her to be a villain, implying that it didn't come naturally to her.
And third, being a paid ninja for hire is not as Evil as killing for the joy of killing (i.e. Crystal again). Therkla had a job, she did it. She didn't ask questions about who Kubota marked.
Maybe it's a borderline case, but it's how I wrote her reactions.