The antagonist was pretty clearly the bald Vulcan guy. The prosecutor didn't think the law was just, but it was her job. Kind of like Riker being forced in Measure of a Man.

I think it was made clear in DS9 and reinforced here that the whole Federation POV was entirely because of the scars on earth of the Eugenics Wars. I feel like it's maybe analogous to the Patriot Act - passed because of a traumatic event, but now decades (or centuries on) kind of hard to justify for anyone, but getting rid of a law is hard.

And the entire point of the episode was the Federation is bigoted against augments, and no - there's no good reason for it. It's about as good as the argument that because Mao and Stalin were atheists, we should ban atheism - as if THAT's what made them horrible people. And there's nothing in the canon to imply that Khan and the other augment war lords were war lords and fighting the wars because they were augments.

I've said other places I think this hypocrisy of the Federation is actually pretty justified in earlier Trek, we may not like it - but it's not because of nuTrek IMHO. Of course, because Prequel, they also can't fix it.