I could be wrong, but IMO, it most likely comes down to the fact that the admins happen to be human beings and these particular communities are just starting to grate on their nerves. Pages and pages of highly upvoted direct attacks rattled the CEO to the point where he thought it wasn't a completely insane idea to abuse his developer privileges to silently alter user content in an attempt to troll his critics. That is a pretty telling sign of frustration.

Whenever the admins make any changes, a certain sub-section of the site goes completely insane and spams the site with tons of threads about how the site is fucking terrible and how the admins are fucking idiots with the common thread among these rabblerousers being that they always happen to hate a particular group that is ruining the site and destroying the indomitable reddit free speech ethos.

You're thinking of 4chan. Reddit has never been that--it's been moderated for many years.

It's always been complicated, though. Alexis Ohanion has repeatedly talked about the importance of Reddit as a censorship-free platform and talked up the company as embodying unfettered free speech.

Obviously that's not true, but major figures at the company have said it from the early days up through very recently. And the difference between moderation (in the "no spam, no personal threats, communities enforce their own rules" sense) and administrative speech restrictions is a big and challenging one.

So no, Reddit has never quite been that, but it's been one of their selling points regardless.