I love this question, as it is very perceptive, focusing as it does on the extent to which this story is influenced by its author's Catholic faith. In a sense, we could argue that this story is much more about grace than it is about evil, but if we look at the characters of the grandmother and the Misfit, we can see that O'Connor conveys a very interesting message about sin and evil that is entirely in keeping with her personal theology.
Christian theology argues that all humans are born as sinners, and whether we commit big sins or smaller sins, we are all in need of grace in order to receive the gift of salvation. The text explores this view through the way in which the grandmother and the Misfit are linked together as characters. Even though we would argue that the Misfit is the "bigger" sinner, the text seems to point towards the way in which both characters are "evil" in the way that they commit sin and both show an equal need for grace. Consider what the Misfit says about this subject:
I found out the crime don’t matter. You can do one thing or you can do another, kill a man or take a tire off his car, because sooner or later you’re going to forget what it was you done and just be punished for it.
Note how this fits into Christian theology. Regardless of the extent of our evil, we are all sinners because we all commit "crimes" of various natures. Whether that is killing a man or lying about taking your pet cat on a journey with you is immaterial. Man's fallen state is something that is explicitly related to our evil condition. All of us have fallen short of how we should behave and act, and all of us give witness to the "evil" nature within us. This is something that must be accounted for eventually, and be "punished for it," unless we receive grace. The epiphany in the text comes when the grandmother identifies the Misfit as one of her children and therefore sees that she is actually just as fallen and "evil" as he is. Evil is therefore a condition that is shown in this story to taint all of us.