"The Conscience of the King" is a better condemnation of eugenics that most Star Trek episodes, because it is avoids the problem other depiction of eugenics in the franchise have: They portray it as a forbidden fruit, something morally wrong that nontheless works.
Admiral Bennett, in the ds9 episode "Doctor Bashir, I Presume", says "For every Julian Bashir that can be created, there's a Khan Singh waiting in the wings – a superhuman whose ambition and thirst for power have been enhanced along with his intellect."
Genetic manipulation is made akin to Garry Mitchell apotheosis in "Where No Man Has Gone Before": it is wrong because giving infinite power to a faillible human make them immoral. (The interesting implication is that it is our vulnerability that is the source of morality.) The ban on "augmented" is a nod in the direction that a society which tolerate eugenics would become unethical, but I agree with the many people who have pointed out that it ends up punishing the victims.
In "The Conscience of the King", eugenic is the folly of an evil man. It turned a catastrophe into a massacre. It served no purpose, accomplished no end.
