It seems perfectly reasonable to me to place limits on any genetic manipulation of people to prevent the effect, whether intentional or not, of creating a class of enhanced "supermen" who may come to feel that their rightful place is in charge. Especially when this has happened before. Bigotry is defines as an "obstinate or unreasonable attachment to a belief, opinion, or faction; in particular, prejudice against a person or people on the basis of their membership of a particular group."
The key question is is this "unreasonable" and clearly the Federation do not think this is so. Remember when Bashir's situation emerged it was his parents who were guilty for taking their child and having him enhanced. He was not sanctioned. Therefore it is clear that while the practice is forbidden. the individuals are not seriously discriminated against. True they aren't allowed to join Starfleet. But real world militaries exclude people on medical grounds all the time. We don't call it bigotry because the Air force won't accept a pilot applicant who is colour blind, or too short to fit the ejector seat.
The key question is is this "unreasonable" and clearly the Federation do not think this is so. Remember when Bashir's situation emerged it was his parents who were guilty for taking their child and having him enhanced. He was not sanctioned. Therefore it is clear that while the practice is forbidden. the individuals are not seriously discriminated against. True they aren't allowed to join Starfleet. But real world militaries exclude people on medical grounds all the time. We don't call it bigotry because the Air force won't accept a pilot applicant who is colour blind, or too short to fit the ejector seat.