There are some parallels between homosexual rights regarding serving in the military. For the longest time, homosexuals were barred from serving in the military. More specifically, the act of sodomy was grounds for dismissal. It was in effect during WWI and WWII, back in a time that the act of sodomy was considered to be the sum of a homosexual male. People just had a fear that if you let gay people into a situation with other gay men, the first thing they would do is try to have sex with them. Being gay defined you more than any other of your attributes. Wanting to serve your country, intelligence, physical fitness all went out the window because "they couldn't risk you losing control and trying to sodomize everyone". We have since realized that sexual acts do not imply sexual preference and sexual preference is just a small part of a person, yet it took until 1993 to settle on "don't ask, don't tell", which still was just skirting the problem and until 2011 (four years ago!) to do away with it completely. That is the fear of the augments, "You can't just let augments go running around starfleet without them trying to conquer everything!" It isn't right to make that sort of judgment.

The difference with Augments of the Eugenics wars were an artificial construction, they were not flukes of evolution. The practice was not barred as a "racist" tactic but as a realization that it was too dangerous to go unchecked, to create humans with this extent of modification from the embryonic level, so humanity was ordered to stop. It's different from using genetic engineering to fix life threatening defects. People don't need to be super men.