Garak had earned (to a certain degree) the crew's trust by the time "Favor the Bold" occurred. There were numerous instances in which Garak commented that people seemed much more comfortable around him during the previous season, so it's not a stretch to believe Sisko would allow him to man one of the bridge stations in a combat situation. It's not as though Garak had anywhere else to go if he betrayed Starfleet, as Dukat would have had him killed had he tried to defect to the Dominion.
What's more, he would almost certainly not have been accepted on Bajor, and it's not clear how the Romulans would have reacted to his presence. They had a non-aggression pact with the Dominion, but they may have made an exception for Garak due to his role in the botched Tal Shiar-Obsidian Order mission to the Gamma Quadrant three years before.