I remember way back when the Internet was new and we were waiting for the finale to air, there was lots of debate about who would get to kill Dukat in the end. Many people (myself included) thought it should be Kira. So I remember being disappointed in how it happened for that reason.
That bothers me, too. I felt like Dukat and Winn clearly have to die, and Sisko and Kira have pretty much equally been adversaries to both of them, so Sisko should kill one, and Kira the other.
Since the end of the series is so focused on the prophets, I would have gone with Sisko and Winn as Emissary vs. anti-Emissary, and Kira and Dukat representing the military conflict that defined the series. It also would be a nice final closure for Bajor, to have Kira be the one to bring Dukat to justice.