Yep, DS9 was less under his control and ignored some Roddenberry dogmas for the better.
If you really
look at DS9, though, it too fits with Roddenberry's idea of a future where a diverse group of people come together for a common goal. Roddenberry established TNG with a "conflict mostly from beyond" philosophy, but in a sense, DS9 adopted this too with the Dominion War with Sisko and the gang eventually becoming something of a tight-knit family. With TNG, it was pretty much there from the start but the DS9 crew had to work to get there.
But I don't view it as something totally different, Sisko did let Garak kill a Romulan senator but he said no to S31.
It was a moral dilemma that I think Roddenberry would actually have approved--To commit wrongs to do something right? Do the means justify the end? Sisko said it best that "it's easy to be a saint in paradise,"
but there was no paradise to be found right then and there.
SISKO: People are dying out there, every day! Entire worlds are struggling for their freedom. And here I am, still worrying about the finer points of morality...