The problem with shutting down the hateful subreddits is that they didn't communicate clearly. In that, they left a lot of room for rumors and speculation about why that sub was shut down for "harassment" when others that seem more harass-y were not targeted. Remember, most users never visited those subs, and weren't in the know about their modus operandi. Those rumors led to the takedowns looking like censorship of distasteful content to many users. If it was censorship of distasteful or rude content, then there are many other subs that should fall alongside those taken down.

I think if they had said that the people in those subs were posting pictures of people and not responding in a timely manner to legitimate requests by aggrieved people portrayed on those subs, the users who don't really care about those subs would have brushed it off.