A problem is the pseudo science makes the supposed moral dilemma less gray and makes the main characters totally unsympathetic.
Its easy to see Phlox using eugenics to justify not helping the Valakians, on the basis that the Valakians are threat to the "natural development" of the Menk and the Valakians need to "go away" before the Menk can truly develop. That logic has some scary parallels to the real world.
Phlox doesn't come off as a alien who is applying different logic to see a situation, he comes off as a cruel and psychopathic monster who is using eugenics to justify letting billions of people die in a plague. I don't see why Phlox being an alien justifies any of that, the Cardassians are aliens and no one is going to say what they did on Bajor was okay because of that fact.