The topic of Genetic Engineering seems pretty wide in the Federation. There's two examples of legal applications of genetic engineering from that page:
- By the 24th century, the United Federation of Planets allowed limited use of genetic engineering to correct existing genetically-related medical conditions. (Either TNG 7x19 Genesis or DS9 5x16 Doctor Bashir, I Presume; the reference isn't clear)
- In some cases, genetic engineering can be permitted to be performed in utero when dealing with a developing fetus to correct any potential genetic defects that could handicap the child as they grew up. (VOY 5x19 The Fight)
Note that both of these are about making people healthier - not better. This is perfectly in line with what the Darwin Genetic Research Station was supposed to have been doing. The children on the station were guilty of nothing more than an overactive immune system. Their weaponization was an accident.
The ban is primarily meant to prevent people like Khan from being created, after all, so using it for health reasons seems like it would be highly regulated, but not illegal.
Memory Alpha includes a theory that what happened at the research station caused a crackdown in the Federation with regards to genetic manipulation, restricting it even further than it was before. However, except for the existence of the station, I don't think there's anything that really supports that theory.