The Ferengi were pretty much depicted as "space pirates" in their first appearances. Roddenberry was still involved with the show at this time and I think that pretty much renders that "rule" void.
It seems that the main thing that Roddenberry was against was depicting the Federation at war. He reasoned that war was something that the humans of Trek would have left behind and therefore there would always be ways for the Federation to settle any conflict without going to war.
He was also really against any internal plotting and conspiracies where the Federation was concerned. The episode "Conspiracy" of TNG's first season was originally going to be about an actually conspiracy that was free of alien influence. According to some sources, Roddenberry wouldn't allow this and it was rewritten to include the alien invasion. It's also claimed that Roddenberry had been screened TUC just prior to his death and when the film had concluded he planned on contacting his lawyers. Others say that Roddenberry enjoyed the movie, despite it's "anti-trek" plot.
The Dominion War arc in DS9 was something that had never been done in Star Trek and it was a big risk. Fortunately, the risk paid off and many consider the arc to have produced some of the finest episodes of the franchise. The episode "In The Pale Moonlight" is considered by some to be the greatest episode of the franchise, despite it being almost completely "non-trek".
Apparently, Roddenberry disagreed with the decision to kill off Spock in TWOK so much, that he was rumored to have leaked the death scene to the media with the hope that fans would boycott the movie. I'm not sure what his motivations for doing this would be, but perhaps not having any decision in killing off a character that he created may have served as a reason if this story is true.