This episode surrounds discovering a new species who is rapidly dying of a genetic defect, to the point of total extinction in their near future. This species is pre-warp but technologically/industrially advanced.
There is a second species, probably of similar ancestry, who live primitively, where there are somewhat treated inferior by the dominant species. They seem to be immune to the disease that is killing the dominant species.
Once they mentioned that the 2nd species' immunity (and certain dependence/inferiority to the dominant species) I kept anticipating that Dr. Phlox would suggest interspecies mating to potentially weed out this genetic defect. It would solve the problem of the 2nd species being treated like inferior, as well.
Unfortunately that suggestion was never brought up and I guess the writer of the episode just wanted to bring up the "We can't play god" theme where you don't intervene technologically/medically with a less advanced species. Honestly you don't need to intervene medically to eliminate genetic defects - it's called diversification with mating. Telling the dominant species to integrate the other 'inferior' species into their own and interbreed wouldn't be the 'playing god' thing. It's just common sense for anyone who has any comprehension of (genetic) diversity.