When ABC aired the "coming out" episode of Ellen Degeneres' sitcom back in the (I think) 1990s, the affiliate in Birmingham refused to carry it. The Huntsville, AL, affiliate carried it with a disclaimer, but they also refused to air ABC's "NYPD Blue" series for years, replacing it for a while with, of all things, "Star Trek: Voyager."
There was an episode of the mostly dreadful second season of the syndicated War of the Worlds: The Series that my local station in Cincinnati refused to carry, so I had to watch it through the staticky signal of a TV station in Dayton, Ohio, 50 miles away. It involved the aliens hiding subliminal messages in a very racy perfume commercial with a totally nude couple in bed together, their bits hidden only by camera angles and posed limbs. It was the show's third subliminal-message plot in two seasons, but the in-show commercial really pushed the envelope even by the standards of the NYPD Blue era.
Though of course, that's a very different thing from refusing to air an episode due to same-sex or interracial content. I think that by the time DS9 did "Rejoined," my local stations didn't carry it, so I had to watch it on a Dayton station too. So I don't know whether that particular episode would've been a problem locally.