I have no problems with Kira commanding the Defiant
, she was Sisko's XO and its his call who holds the post on the ship as well. I would have liked a little more consistancy though, as Worf is seen in the role of Defiant
Numbah One whilst Kira is sitting right there, then in the last episode of S6 she assumes command when Sisko is overcome with the loss of the Prophets.
Plus there is the fact the Bajor is petitioning for UFP membership, which would likely see the Militia fold into Starfleet (well most of it anyway), so it would make sense to get some of its officers trained up on Starfleet systems and designs before that happened.
Personally, I'd rather follow Kira's command than Worf's.