Well, I've never liked Flannery O'Conner. I thought she was a creepy woman who wallowed in mental illness and buzzed over sores like a fly. She's the perfect example of what Catholicism will do to a potentially logical mind, and her thesis (which seems to give the false choice that there is either God or apathy) is just an example of the limitations placed on the mind by religion. There is an objective truth, and it has to do with the physical world. People who cannot accept that end up either emeshed in religion as a self-protective device, or flailing against it because they hate what they perceive to be the only alternative. It's pretty tragic.
The human mind, or what small percentage we use of it, is incapable of imagining the size of the universe, its origin, or even where it is, which is why I disagree with you assessment that everything should be viewed in concrete physical temrs. It simply isn't logical to believe that science is capable of unlocking every mystery in the unviverse and of understanding everything in a pure material way. There are certain things we were not meant to understand...are not capable of understanding.
I do not think her choices were faith or apathy alone, as Motes demonstrates rebellion. I wouldn't call faith self-protective either. I would call it a love affair [Stop rolling your eyes!]. If a person hates love, I would have to ask...why? The stubborn will that enjoys the easiness of subjectivive reality is my answer. =)