I'm a vegan so experienced bean eater. There are a couple things I found that help, but they do come at a cost of flavor or texture:
Soak and rinse, but the soak water should be boiling when the dry beans go in.
Alkaline. Sodium Carbonate (baking soda) or calcium hydroxide (lime) work. Throw away the cooking water. This has to be done carefully, as too much of either can give the food a mineral taste and/or dissolve the beans entirely.
Fermentation also works. Lactic acid (like kimchee or pickles) helps a little. Koji (either added or grown on the beans themselves) helps a lot. Both will have a big impact on the flavor and what the beans will be good for in the end.
A lot of these problems are already managed by nurses or clinic assistants. It's pretty rare to get a lot of face to face time with an actual M.D. Certainly this is true the more you look at poorer communities.
Resources on wild pig management usually recommend trapping or baiting rather than trying to shoot them. Shooting at them with a semi-auto while they are fleeing is a particularly cruel way to address the problem, as you're not making clean kills in this sort of situation.
Literally all of the problems you mentioned existed before GMO was a thing. Companies have been patenting varietals since the 1930's. Patent trolling in agriculture is also quite old. E.g. the yellow bean patent debacle:
Soak and rinse, but the soak water should be boiling when the dry beans go in.
Alkaline. Sodium Carbonate (baking soda) or calcium hydroxide (lime) work. Throw away the cooking water. This has to be done carefully, as too much of either can give the food a mineral taste and/or dissolve the beans entirely.
Fermentation also works. Lactic acid (like kimchee or pickles) helps a little. Koji (either added or grown on the beans themselves) helps a lot. Both will have a big impact on the flavor and what the beans will be good for in the end.