I think what stands out more is when the DS9 crew leaves on the Defiant, they essentially left the command structure at the station empty. I'm sure there's a secondary crew and other senior staff on the station that's not part of the main cast, but from my perspective none of the senior staff remained to deal with possible emergencies.
Ha, yeah that always seemed odd to me as well. With the importance of the station and the continual threats facing it, you'd think Starfleet wouldn't want the entire command crew taking off on missions to the Gamma Quadrant all the time.
As for Kira, I didn't mind her commanding the ship, but I do wonder how she could be remotely qualified for it. Captaining a starship seems like something that would require a lot
of training and experience, and service on other ships-- and isn't something you could just pick up through a few online courses.
Obviously she handled herself well and seemed to have good instincts, but I can't exactly imagine her captaining the Enterprise D, for instance, or dealing with some of the crises Picard had to. She was a bit too much of a blunt instrument for that.