It is implied in the movie that atheists are as they are because they 'hate God/gods' because of some personal tragedy. But by definition atheists have no belief in any gods, so would harbor no such hatred towards an imaginary entity.
If Dr. Sol Harkens were truly the 'world's leading atheist' he would have been satisfied with the doctor's explanation of his visions and would not question further.
Dr. Sol Harkens rediscovers his lost faith after a near-death experience in which he has a vision of his dead son. However, biblical, or more specifically, Christian, faith is usually defined as 'the evidence of things not seen'. If you have evidence, you don't need faith.