I never really got the argument against augments (in universe as well as from the writers).
All the humanoids in Star Trek are the result of genetic augmentation anyway.
The whole "eugenic wars" thing always felt like a cop-out because the writers were to afraid to tackle a controversial topic during the actual show and pushed it into the past in a "we already had this discussion" kind of way.
I would argue that the bad reputation that eugenics got by being associated with fascism is very detrimental to societal progress.
Before we understood genes and could manipulate them, the "solutions" (e.g. sterilization) to debilitating genetic disorders were very cruel.
But this has changed with the advent of genetic screening and gene therapy.
People are so reluctant to accept the good that these technologies can do that we are dooming future generations to unnecessary suffering.
The first time I heard of diseases like cystic fibrosis, Duchenne muscular dystrophy, and Huntington's disease I was very curious why they were not being eliminated by genetic screening.
People act like we would immediately create a second class of people like Khan if we allowed more direct intervention but this is simply not true.
There is a world of difference between eliminating horrible diseases and creating super humans.