According to the article, the National Audubon Society is keeping their name, which I think is probably for the best.
Renaming birds named after people is a good idea too, but it's nice to be able acknowledge that people can do amazing things that deserve recognition while also doing terrible things that deserve to be condemned. The blanket painting of people as either heroes or villains is childish and doesn't reflect reality or the complex nature of what it is to be human.
Renaming the National Audubon Society would make about as much sense as renaming the Washington Monument. A history of slavery is something that has tainted the pasts of human civilizations all over the globe and slavery continues to be a something we all profit from even today (which is something I think we may all be judged as "evil" for). In the US it's a very large and shameful part of our history, but I think it's probably better to face that openly rather than to try and sweep that shame under the rug by erasing anyone involved.