Re: EFB options
Now that deserves more information. On a local level, feral bees would tend to stabilize genetics meaning that bringing in managed bees would increase diversity "OF THE FERALS". On a regional or nationwide basis, would you argue that the managed or feral bees have more diversity? Be careful with this one as there is indeed a study showing very low genetic diversity in commercial queens.
This is more telling.
"These findings suggest that genetic diversity is positively associated with immunocompetence in feral honey bee colonies, and that the benefits of genetic diversity are obscured in managed bees, perhaps as a result of artificial selection. We hypothesize that high genetic variability provides the raw material upon which natural selection acts and generates adaptive genotypes in unmanaged populations. Feral populations could be useful sources of genetic variation to use in breeding programs that aim to improve honey bee health."
Seems to me that this counters most of what you attempted to posit.
As for selecting for EFB resistance, that would be fairly easy to do empirically. Set up disease challenge experiments. One way it could be done non-destructively would be to capture a test population from each colony and challenge them with EFB to see which are least affected. Then breed from the colonies that have the best test results.
The study you quoted is testing for "immunocompetence". While it is a valid research result, this was not shown to correlate directly with EFB or AFB resistance. It is kind of like having general disease resistance to bacteria, but maybe still susceptible to viruses or vice versa.
This does not come even close to the common house fly which has resistance genes far more advanced than most other insects. If the honeybee had the resistance genes of the house fly, we might currently be overwhelmed with hordes of honeybees.
NW Alabama, 50 years, 20 colonies and growing, sideliner, treatment free since 2005, 14 frame square Dadant broodnest