In this statement, Miss Maudie is making a comment on some of the "Bible thumpers" in town who use the Bible to criticize, condemn, and punish those around them. Specifically, she is thinking of the "foot-washing Baptists," a particularly strict sect in Maycomb, and the ways she has seen them misuse the Bible for their own aims - hurting others in the process.
Miss Maudie herself has come under their condemnation for spending too much time in her garden. According to them, "anything that's pleasurable is a sin," and she should be spending more time studying her Bible. Scout finds this criticism rather surprising since Miss Maudie can quote the Bible very well and clearly knows her scriptures. She also is the kindest neighbor to the children and certainly seems to understand the concept of showing Christian love to others more than the footwashers or the gossiping Miss Stephanie do.
However, Miss Maudie is especially thinking about Arthur "Boo" Radley when she says this. She recalls him being a polite young man, and she thinks it's very sad to see what has happened to him as a result of his parents' strict religious beliefs. When he got into trouble with his "gang" many years before, the others boys were sent to reform school, but Arthur's father took it upon himself to punish his son in his own way: with a kind of "house arrest" that isolated his son from everyone in town and kept him from any forms of misbehavior, but also any forms of pleasure or social interaction. Over the years, "Boo" developed into the social recluse he now is, fearful of people and society and afraid to venture out of his house.
While clearly "whiskey" in the hands of the wrong man, such as Bob Ewell, can be a terrible thing - and leads to all sorts of evil in this book - Maudie recognizes that in many cases, Bible thumping can be worse than whiskey in destroying the lives of those in its wake.