Sisko would have punched him in his mouth every other show.
Honestly, I think every other show Tom would have tried to break someone out of the brig then Sisko would have pretended to try to stop him but really turned the other way until the person escaped then yelled at him.
Sisko gave several speeches on what type of person it takes to wear a Starfleet uniform, the honor it takes and what it means to be a Starfleet Officer. Tom didn't have those traits. It would have been a serious insult to Sisko having a traitor like Tom on his team and wearing a Starfleet uniform. We saw how Sisko felt about Eddington being a traitor. He wouldn't have looked the other way at Tom's infractions, he would have been looking for ANY excuse to get him off his station.