All in all, I think this was a pragmatic move. I am not a fan of this "CEO = literally the company" logic, though. I saw no reason to believe that he would use Mozilla to further an anti-gay agenda.
I agree. However, it's a little weird if you say you are a company who values diversity and different lifestyles but you have a CEO who is openly against a particular group of people. That kind of contradiction at the very top makes things weird.
If you're worried about his future career, I understand. But if he changes his mind he can equally talk about it with potential employers/partners. If he doesn't, then he gets to live with the consequences of his choices the same way someone who is out about their sexuality does.