If I remember right, DS9 was the last show that Mr Roddenberry had any input into. He was involved in the early stages of its inception, but passed away before the show actually came to life. It's entirely possible that Dukat was part of his vision for the show.
It definitely took on a life of its own under its subsequent writing staff, though - Ira Behr, in particular, brought a rather profoundly dark new angle to things, like having Sisko's plot lure the Romulans into the Dominion War; even the war itself was something of a departure from what was once envisaged, and it earned mild criticism from the late Mrs Barrett-Roddenberry for detracting from Trek's former vision of optimism and light in the future. Still, I feel that DS9's later seasons were a superb glimpse into the grimmer, less selfless and utopian side of 24th-century life, love and war. Dukat definitely played a big part in that.