Jane enjoys a friendshiup with St. John Rivers until he asked her to go to India with him as his wife. He begins by admonishing her for being happy with her life and for not straining herself to work against the sins of the flesh (those being comfort) and to work to use her talents to their fullest.
He attempts to persuade Jane that God intended her to do His work and that this included marrying St. John and traveling with him to India. However, she answers "no" because she knows he does not love her, that
He prizes me as a soldier would a good weapon; and that is all (Ch. 34)
Jane has no argument with St. John. She knows he is a strong, pious, dedicated, intelligent and able man. However, she will not deny herself true love. She has always been true to herself and completely dedicated to God's guidance.
My spirit," I answered mentally, "is willing to do what is right; and my flesh, I hope, is strong enough to accomplish the will of Heaven, when once that will is distinctly known to me. At any rate, it shall be strong enough to search--inquire--to grope an outlet from this cloud of doubt, and find the open day of certainty (Ch. 36).
Ultimately, her rediscovery of Rochester makes her decision seem less important. Her true love is alive and needs her. Jane tells him the absolute truth about St. John - he has many admirable qualities. Jane does not consider her NOT loving him a flaw. Nonetheless, her conscience will not allow her to marry him.