That twist is easily the worst decision they made in the entire history of DS9. It completely trivialized all the good things established about his character and it made absolutely no sense with his established traits.
It also established a systematic prejudice against children enhanced beyond their own control, which goes against everything established about the Federation. And IF they wanted to do that, they should have had a story about genetically enhanced kids who leave the Federation and take high paying Ferengi jobs or get recruited by the Romulan military. Or at the very least had other genetic kids say "Hey WAAIT a minute, I've been blacklisted my whole life, this Bashir gets a pass just because he managed to hide it long enough? Fuck that, if he gets to join Starfleet so do I." Instead all they did was have a bunch of lovable traitor lunatic geniuses who didn't challenge the system in any real way. If they had treated it a little more like telepaths in Babylon 5 it would have worked better. But instead they just made it this systematic prejudice that nobody questions and everyone goes along with. That was the worst of both worlds, it made the Federation less likable AND it whiffed an opportunity to say anything interesting about human nature.