Presumably the parents approved a legal adoption for the yakuza guy before offing themselves. That in itself might be unrealistic though if there's an investigation into the appropriateness of the adoption, I would assume that's typically pretty strict in real life.
The crush was crying because he knows her parents killed themselves, which is just an absolutely terrible thing to happen to a young child. He's crying in empathy for her, and also because her callousness in the face of their suicide confuses and terrifies him.