Up to this point we've had hints enough about Fanny's feelings for Edmund, but I think this passage is the most definitive indication. Edmund comes in and says he wants and values her advice, which thrills her, but by the end of the chapter she has "seen [Miss Crawford's] influence in every speech." In a way, Edmund sort of pays lip service to Fanny but makes his decision for Miss Crawford, indicating that Miss C takes precedence in his heart. I think Fanny experiences both a broken heart and must feel a bit like she is losing her one true friend, now that she's alone in her objection the whole scheme.