How do Stanley and Mr. Sir get even after the Warden punishes him in Holes?

I assume you are referring to the scene in which the Warden hits Mr. Sir and scratches him with her nails coated in varnish containing rattlesnake venom. Stanley does not get punished for stealing the sunflower seeds, and the Warden punishes Mr. Sir for bothering her with an insignificant, petty theft. Your question implies that Stanley and Mr. Sir worked together to get even with the Warden, which is not the case. Mr. Sir punishes Stanley by depriving him of water for an entire week.
In terms of Stanley's actions, him and Zero finding the long-lost treasure of Stanley's great-great grandfather can be interpreted as getting even with the Warden. The Warden had been searching for the treasure since her father forced her to dig holes as a child, leading to her making the juveniles dig holes at Camp Green Lake. Not only is the Warden deprived of the treasure that had taken over her life, Camp Green Lake is down by the Attorney General. At the end of the novel, the author mentions that the site will become a Girl Scout Camp in the future; assuming Mr. Sir will be required to work there due to his parole conditions, this is also a result of Stanley's and Zero's discovery of the treasure.