The chapter that you need to focus on is Chapter Twelve of Book the Second, entitled "Down." It is in this Chapter that Louisa, having said to James Harthouse that she will run away with him, runs instead to her father and, using very harsh words that cannot be misinterpreted, curses the way she was brought up and blames it for the emotional confusion she is experiencing at this stage of her life. Note what she declares to her father about James Harthouse and her relationship with him, and how she comments upon her upbringing:
"This night, my husband being away, he has been with me, declaring himself my lover. This minute he expects me, for I could release myself of his presence by no other means. I do not know that I am sorry, I do not know that I am ashamed, I do not know that I am degraded in my own esteem. All that I know is, your philosophy and your teaching will not save me. Now, father, you have brought me to this. Save me by some other means!"
Thus it is that Louisa's breakdown comes as a result of recognising the complete inability of a fact-based upbringing to save her from a situation which has arisen in her feelings that she does not know how to handle because she never was aware that she had those feelings in the first place. The facts of her father have resulted in her emotional stunting in her adulthood, and the attentions of James Harthouse have exploited this.