The show was made for syndication, so it wasn’t airing on any particular network. It was Rick Berman that had the issue with it on Deep Space 9, and both he and Brannon Braga (aka “Bermaga”) that had an issue with it on Voyager and TNG. Both of them are known homophobes. 
But even what happened with Ellen in 1995 and Will and Grace in 1997, didn’t make much progress on Star Trek. There was even a scene with lieutenant Hawk and his husband in Star Trek first contact that was cut per Rick Berman‘s orders. 
edit: sorry for the multiple replies! lemmy is being weird