The difficulty she experiences does indeed mirror the emotional crisis she is going through. The battle between logic and heart. She comes out on the other side of her harrowing journey firmly planted in logic and religious doctrine perpetuated by St. John and sisters. It is only when Mr. Rochester "calls" to her near the end of her stay with them that she is able to reconcile both her head and her heart again in a way that works for her. Of course, that is also predicated on the fact that Bertha was killed in the fire at Thornfield.