It's always seemed to me that Sisko was on the fast-track to getting a ship of his own (much as Riker had been) prior to Jennifer's death, as he had already served as first officer twice. Her death was such a profound blow, however, that it sent his life into a tailspin, and caused his career to stagnate. By the time Starfleet was ready to assume control of Terok Nor
, Sisko had been promoted to full commander- one step from a captaincy- but he was so frustrated and unhappy with his life in Starfleet that he was considering leaving it behind.
Having served with Sisko aboard the Okinawa
, Thomas Leyton understood the younger man's potenetial. As an admiral, he was almost certainly aware of Sisko's unhappiness with Starfleet, and recognized that offering a ship to someone wasn't invested in such an assignment would not be prudent.
Enter Deep Space 9
, a space station built by Cardassia, located near a backwater, low-priority planet. Leyton likely recognized that recommending Sisko for this assingment was a low-risk move. Bajor was unlikely to join the Federation, so Sisko's leaving wouldn't impact the Federation as significantly as if he were commanding the Enterprise
, or handling another assignment of great importance. However, if Sisko were able establish a rapport with Bajor- something no other Starfleet officer had accomplished- it would ensure him of a captaincy and restore his career to its original track.