Exactly. For example, "fixing" MTHFR genes could lead to an increased risk of developing lymphoma: https://www.ncbi.nlm.nih.gov/m/pubmed/15551285/

The degeneracy of a given allele is relative to the phenotype of the organism and also the organism's environment. Sickle-cell confers survival advantage in environments where malaria is endemic, but is considered a degenerate allele in environments without malaria.

>Not if the people with the degenerate version also have another mutation that interacts.

Is this common? An uncommon detrimental variant that is slightly-mitigated by another uncommon detrimental variant, such that the removal of one makes the other worse isn't the type of thing I would expect to come about through natural selection.