“Debating” an anti-vaxxer on Joe Rogan’s show would (as the old saying goes) be like playing chess with a pigeon. No matter now great you do, the pigeon will knock over the pieces, poop all over the board, and strut around as if it won.
I’m all for open debate when the other side is acting in good faith, but antivaxxers don’t act in good faith. At best, you’d refute every one of their claims , but even then they wouldn’t change their view. They’d just (as you said), release an edited video showing you either stumped by their anti-vaxxer genius or (worse) agreeing with them.