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It would seem that she sent Joe in her place. She was the one who did all the work in the house.
"My sister having so much to do, was going to church vicariously; that is to say, Joe and I were going. In his working clothes, Joe was a well-knit characteristic-looking blacksmith; in his holiday clothes, he was more like a scarecrow in good circumstances, than anything else."
The irony is that Mrs.Joe pretends to be the morally upstanding Christian yet she doesn't attend church.