Miss Maudie is making a clear distinction between a good man (i. e. Atticus) and a bad man who professes to be good (Mr. Radley). Miss Maudie claims that Mr. Radley is a foot-washing Baptist. In other words, he is very strict and takes the Bible literally. Miss Maudie adds that foot-washers believe that anything that is a pleasure is a sin. Consider Arthur/Boo Radley's life in such a house. Mr. Radley professes that he is a man of God. Apparently, he was so strict that he drew all the joy out of Arthur's childhood and subsequent life.
Even if Atticus were a stumbling drunk, he would still be a better man than Mr. Radley. Atticus doesn't need to show off his Biblical knowledge nor does he need to prove himself as a spiritual beacon. His character is shown by how he lives. He constantly thinks about other people. He is always looking at the world through the eyes of others in attempts to understand, empathize, and help. Mr. Radley, religious as he may be, never really does this with his son. In short, a hypothetically drunken Atticus is always better than a sober Mr. Radley.
In a later chapter, the women of the Missionary Society claim that they support the Mrunas but they aim to keep the black citizens of Maycomb in their subservient place. Using Miss Maudie's logic here, a drunken Miss Maudie is always better than these hypocrites. Although this goes beyond the context of that conversation between Scout and Miss Maudie, the point is the same.