I imagine that (at least for the foreseeable future) genetic engineering will only be targeted to modifying SNPs (and other mutations) that unambiguously cause diseases.
If we'd had the option to remove the gene that causes sickle-cell anaemia from the population, wouldn't we have taken it? Which would have meant we then didn't have the malaria-resistant population that now exists due to that same gene.
On the other, we’re currently exploring ways to wipe out malaria carrying mosquitoes.
On the third (genetically modified :P) hand, easy gene modification will probably lead to a similar patch-cycle as we already have for software.
On the fourth hand, thanks to the typical decade long testing cycle for medicines, the worst parts of this hypothetical future are likely to happen around the same time we get full-mind uploads.