Let's also remember that the Defiant
isn't exactly an example of standard Starfleet practice. The lemon of a prototype ship was given to Sisko for a suicide mission; that the ship ended up surviving the mission was a surprise to Starfleet, and probably to Sisko as well. It's essentially a piece of bureaucratic jetsam now, much like the whole DS9 affair: exception piled upon exception.
A more orderly starbase closer to home would no doubt have a more orderly commander, with a thing or two to say about how his or her attached ship assets are crewed and used. But Sisko revels in his exceptions, and Starfleet is delighted to have this "special arrangement" where a low-ranking outsider manages to become the de facto religious leader of the entire planet, even if this means turning a blind eye to various rules and regulations.