Mrs. Merriweather is calling the Northerners hypocrites. Her reasoning is that in the north, they've set the blacks free, say they're equal, but still won't sit with them at a lunch counter. That's hypocritical, according to Mrs. Merriweather. Mrs. Merriweather (a member of the church missionary circle, a group that is supposed to be pious and doing good) believes they are NOT hypocritical in the south, because they think blacks are dirt and treat them as such.
The missionary circle meeting is full of hypocrisy and irony like this. Note Mrs. Merriweather's name--Merry Weather, like Good Weather. It's ironic because she is the one that is full of hypocrisy and criticism.