Is Flannery O'Connor criticizing Christianity?

I don't think O'Connor is criticizing Christianity so much as she is criticizing Christians like the grandmother. The grandmother places so much importance on acting and dressing like a "lady" and laments the lack of "good men"; but how does she define "good"? It seems that she is addressing a particular social class of individuals, specifically, white men.
For real Christians who live their faith, however, what makes a good man? A good man is one who is honest and trustworthy, who is generous and merciful, who is kind and caring. Class, race, wealth: none of these things have anything to do with being truly good.
Perhaps, if people like the grandmother focused more on being truly good rather than upholding some antiquated notion of gentility that relies on racism and sexism for cultural legibility, then people like the Misfit—individuals who will never check the "right" boxes to qualify as "a good man" by the grandmother's definition—will not be devalued and exploited by society. I won't say that she deserved what she got in the end. However, she did finally come to realize the connection between her and someone like the Misfit, instead of continuing to view him as so different from her.