Just put them in a retirement home for the disabled/retarded where a computer and volunteer staff can look after them.
Just because the federation doesn't have them put down don't mean they can all complete training in starfleet academy.
The real question you should be asking, is why isn't places like section 31 or starfleet HQ full of genetweaked superintellects?
Sure, eugenics war's and all that, but in a society made up of many different races, you will inevitably have some races being smarter or dumber than everyone else (Packled's for example) so why is there still such a stigma attached to genetically engineered people? And more interestingly, do all the member races of the federation share this sentiment, or do some allow it?