At first, Atticus doesn't punish the children, he just offers them a firm warning. In fact, in chapter 4 when he first catches the kids, he just lets on that he gets they are doing something about the Radleys. The kids do not understand or think that he specifically told them not to play the game anymore. At this point, if anything, he discplines them by not letting them know that he really absolutely knew what they were doing which leaves them guessing and forces them to think about what they are doing and make a moral decision on their own.
When Atticus catches the kids in chapter 5 trying to get a note to Mr. Radley on a fishing pole, he yells at them and envokes the fact that they were doing something wrong by playing the Boo Radley game earlier, but he uses it as a part of a whole string of things they were doing to upset the Radleys, particularly Boo:
You stop this nonsense right now, every one of you!"
At this point, all it was is a lecture. It could have been worse.
Dill and Jem are particularly fascinated with the mysterious Boo Radley. Dill writes Boo a note and tells Scout that
“We’re askin‘ him real politely to come out sometimes, and tell us what he does in there—we said we wouldn’t hurt him and we’d buy him an ice cream.... I figure if he’d come out and sit a spell with us he might feel better.”
With Scout along to help, the three children stick the note on the end of a fishing pole with the idea of trying to get the note to Boo through a side window of his house. Instead, they come face-to-face with Atticus, who is less than pleased with this game.
Atticus tells them to stop "tormenting" Boo. He tells them to allow Boo his privacy and informs them that if Boo wants to come out, he'll come out. He tells them not to play the "asinine game" he'd seen them playing earlier when they were acting out "Boo stories," and not to "make fun of anyone on this street or in this town."
Jem protests in response to Atticus's general demand; he says that they were not making fun of or laughing at Boo. Atticus retorts that when Jem says they weren't doing this to Boo, Jem has, in fact, confessed. Jem, Scout says, has "been done in by the oldest lawyer’s trick on record."
Atticus's form of discipline is to trick Jem into a confession and to tell the children point blank to "stop this nonsense right now." He has trouble keeping a straight face: "Our father’s mouth was suspiciously firm, as if he were trying to hold it in line," Scout writes. Nevertheless, while possibly amused by some of the antics, Atticus makes it quite clear that the children are not to treat people the way they have been treating Boo.