O'Connor uses nature as a buffer between what appears to be and what really is. As a Christian believer, O'Connor sees beyond nature (the sun, clouds, and sky) to see the supernatural (God, heaven, afterlife), but she sets her fiction in only the physical world as witnessed by non-believers who cannot see beyond. So, to her characters there is no physical signs of God's handiwork in the universe. To them, the world is Christ-haunted. What used to have meaning (sun = Son of God) is now just a sun.
What O'Connor Really Believes:
Nature is good, created by God for man's use
What is reflected in O'Connor's Fiction:
Nature is often hostile, evil, a source of temptation, insensate