It's not just about free speech, it's about his position of leadership in those organisations. He needs to either moderate his public viewpoints in order to look out for the best interests of the people there, which is what a good leader would do, or he needs to resign because he clearly doesn't understand his job.

When you're the head of the FSF, or any other organisation really, you can't just be some kind of agitator, throw out a bunch of controversial nonsense, and then expect it to not look bad for the people you're supposed to represent. It's not an "assault on free speech" to get kicked to the curb for making your organisation look bad, it's cause and effect.