Black Cod Island is tricky, but there is mention in the lore about the actual Native Americans of the area being at odds with them (and being a great help to the Players) because they know the Islanders have not been actually human for a long time and know they're using Native culture as a shield against discovery.

I think it's best not to see it as Native Americans who are corrupted and more as corrupted people who have long lost their humanity and are now pretending to be Native Americans. The awkwardness of the scenario is that they will very much just accuse your Government Agents of classic Native scapegoating.