"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.
Of course I understand that Star Trek originally tackled issues like racism and sexism. But DS9 wasn't made in the 60's. Many issues that were extremely relevant back then, like racism, were not nearly as relevant in the 1990's. I'm not saying that racism had entirely been eliminated by the time this episode aired, but it wasn't an issue in the way it was back in the 60's.
Also, in your first paragraph you said that racism was only the backdrop of Far Beyond The Stars, and then in your next paragraph (the one I quoted) you stated that this episode was praised for its message about equality and diversity. What exactly were you trying to say? I would answer the question myself, but I don't care for this episode, nor do I understand why this episode is so widely praised.