I completely agree with you on Far Beyond the Stars. How many times did the writers need to shove their message about racism down our throats? After five minutes of it I grew really tired of this episode. Frankly, I don't understand why so many people praise it and call it one of the best DS9 episodes ever.
Far Beyond The Stars isn't about racism as it is about finding faith. The story starts out by showing Sisko suffering from a lack of faith to survive the war, Benny is writing a story that he has faith will inspire others. Racism is the obstacle that that is testing his own faith to survive. In the end, the story ends with Sisko regaining his faith. Racism is just the back drop, no different space is the back drop from Trek to tell stories of social & political injustices.
"Far Beyond the Stars" is exactly what Gene Roddenberry created Trek for. Seriously, have you forgotten that Roddenberry was creating Trek during an American revolution when Civil/Equal rights was a huge issue? It's the exact reason why he wanted a multi-racial/mulit-gender cast. Trek is about understanding equality and diversity. That is why it gets praise and rightfully so.