So he's never been a partner and doesn't work "very closely with the companies." Yet he's still affiliated with YC?

Actions speak louder than words: drop him or acknowledge that YC at some level acknowledges his views (this isn't bad, or good, just something that should be done in my view).

Even something as simple as "we acknowledge that people have differing political views, yadda yadda... would be sufficient).

Why say anything about him? Well, clearly he's the elephant in the room. They should acknowledge this and move on.