This is a great question. Flannery O'Connor was a very devout Christian and thus it is perhaps strange that her fiction contains such violence. Yet, from her perspective the violence that she writes about is specifically to highlight the fact that our spirits live in a temporal world. The violence indicates the way that the civilisation and culture we live in is "civilised" only in its veneer - delve to deep and you come across the violence that we are all subject to.
In this great tale we see that O'Connor presents us with two characters who in their separate ways are shown to be capable of redemption. The grandmother, in spite of her selfishness, experiences a moment of grace when she recognises that the Misfit is human just like her, when she calls him one of her "own children." The Misfit likewise shows that he recognises that there is no pleasure in life at all. Killing no longer gives him happiness, which suggests that he too is capable of change.