Rick Berman and Michael Piller would've had a fight on their hands if Gene Roddenberry lived; but the writing was on the wall, so they were able to develop DS9 without having to worry about what would've happened.
The first two years of Deep Space Nine, "The Maquis" aside, are pretty TNG/24th Century century Starfleet on the frontier and exploring new space, and with really little focus on the Prophets or Bajoran religion. Roddenberry would have pushed to tone down Sisko's antagonism in the pilot and yes to have more sense throughout that Starfleet was improving the station and the planet but otherwise he probably wouldn't have had much to object about, but he probably would have very much disliked the Maquis and the Dominion and going to war with them (and the increasing focus on Bajoran religion).
Maybe this is controversial, I think Piller genuinely respected and tried to stay true to Roddenberry's TNG vision/vision of the future, he didn't see the first two years of TNG as some big failed experiment or crazy stupid limitations (though the overall results were flawed and could be improved), he saw the vision and its limitations, constraints as challenging but worthwhile and rewarding to making good shows.
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