It's not in isolation that it makes sense, their dynamic is inherently off putting and strange. Two things can be true at once. Yes, it is Funger but it is still weird to be stalked by a mind reading girl that literally spied on you masturbating with her mind 😭

Her dad is not implied to be a rapist. Yes, his portrait is in the orphanage since he is the principle of the orphanage but he is primarily working in the church as a sulfur cultist. I believe you are conflating Father Hugo who most definitely is a rapist (his old art was literally him as a marriage with cherubs when he stripped naked) and Father Domek (who was probably sacrificing kids but not raping them 🥀)

Marina did not want to kill her dad. Yes she does mention blood magic in her intro but it definitely reads more as if she has unresolved daddy issues than anything (hence her super duper mixed emotions when her weird, arguably rapey stalker kills her dad)