I agree with alot of what you say here. In many ways DS9 is the best show of all of them, as you so perfectly illustrated with your post. But it's also kind of the worst Star Trek show. Star Trek was always about exploration, which is the weakest element of DS9 by far. So many episodes of the show are set primarily on the station, like more than two thirds as I recall. There are a few exploration episodes, especially after they get the Defiant, but it by far has the least exploration of all of the Trek shows that I've watched. People always say that Roddenberry hated DS9, and I can understand why. The lack of exploration, coupled with the show's religious and war themes were the antithesis of Roddenberry's viewpoints, but that's also one of the reasons why I like DS9 so much, it's not afraid to show that the Utopian peaceful society of Roddenberry's dreams couldn't exist without the occasional war to protect said Utopia. It's also not afraid to call out Roddenberry's views on religion, which I like a Christian myself.
You see, I believe that DS9 maintained the premise of Star Trek, except it substituted some of the episodic exploration with a deep dive of multiple cultures and races. Whereas TOS and TNG were content to put a bow on a single episode's message as the aliens of the week conformed with the writers' needs, DS9 went ahead and wallowed in all the nuance of all their choices, seeing them through to the end.
I believe this all is very much in line with Star Trek as it explores the ethics. It just does so in long form. Whereas TNG could introduce the Bajorans and dismiss them within an episode once Ro Laren's character go her backstory, DS9 stayed there and probed the wounds of a planet recovering from not only years of repression and murder, but the self-inflicted wounds of the violence they'd committed to end the occupation. We got to understand the strength they drew from their religion and how their faith made them vulnerable to those who would take advantage of that faith.
And that's to say nothing of the meticulous reading of other cultures such as the Cardassians, Klingons, Ferengi, Dominion, and even the Federation that keep getting circled back to time and again.
As for Roddenberry, hating DS9. I'm sure he would have as his buying into the lore of Star Trek as some utopian paradise hamstrung TNG in its early days and produced arguably the worst season of the entire franchise. Sadly, the show, like the movies before them, needed to be wrestled out of his hands in order to succeed.
All that said, Roddenberry died over a year before the DS9's first episode aired, so he couldn't have had much of an opinion of it.