Sister is not raped. She is impregnated by Dr. Thomas Stone. The event is, certainly, mysterious for a time. Eventually the story is revealed that in a fit of drunken delirium, Dr. Stone and Sister lay together.
The forbidden love between the nun and her mentor is never realized until Thomas has a lapse of judgment during one of his drinking binges, but afterward the two continue to pretend that their affection for each other is strictly professional.
Stone is unable to save Sister's life because he is so attached to her (in love with her). He is unable to remain in Missing to raise his two children because he blames them for Sister's death. He feels that the children killed their mother, the only person Stone ever really loved.
Though Stone does have contact with his children later in the U.S., he never becomes a father to them.
But some holes cannot be mended—wounds that divide families—and it is the task of a lifetime to fix what is broken.