I think Reddit's IPO is the main reason the admins are taking a harder stance.
Venture capitalists are unlikely to care about an anti-vax subreddit as long as they get a good return on investment (or useful data harvesting). They will care if various parts of their investment can go dark at the whims of people who don't work for reddit. Especially when six people control a fifth of the top 500 subreddits. It's not like a dodgy executive where investors can petition the board to have them removed, it's just a volatile platform.
If I were the reddit admin team, I'd remove the ability to make subreddits (over, say, 5,000 subscribers) private/approved submitted only on the basis of "synergising communities and allowing for a more diverse and dynamic discussion base". Throw in a couple of new tools for the jannies to deal with brigading but stress that they don't own subreddits and can't unilaterally decide to tank their community because they're angry about something. If you've got a good reason to ask a sub to go private, the entire mod team can go contact an admin to do it for them. Or at least update the ToS to state that privating a subreddit out of protest is a bannable offence because it negatively impacts user experience.