I payed attention that the book starts with Charles and ends with Bovary-daughter.
Though Emma is the main protagonist, she does not start and does not end the story. It seems that the world managed without her in the beginning, and goes on when she dies.
I also spotted an irony in the following conversation:
I actually can see Flaubert behind this priest, smiling to himself, when writing these lines.
Eventually, it seems that he portrays Emma like a hurican, who comes and goes, who is very egoistic and thinks herself as the most important creature in the world, - but nobody understands her, poor thing The life goes on with or without her and there are troubles more serious than her broken hart
I read this part this morning (yes I am behind) and I didn't read that at all. I read it as the priest being too preoccupied with other things, such as finishing Madame Bovary's sentences, to realize that she needs spiritual/emotional guidance which she needs but he doesn't give.