While reddit stated they weren't banning an idea, only the subreddit, alternative subreddits that popped up on the same topic were also shutdown. The belief is that the idea leads to negative unacceptable behavior, and thus they have actually banned the idea, not just the subreddit.
A more community minded approach may have been better, along with threats of working with law enforcement on matters of real-world harassment. This segues right into the next issue of poor community management and oversight. Poor tools & poor admin oversight of subreddits until they are too big to handle in a graceful fashion. Instead of working on these issues, they fired more staff.
All of these actions may have actually been completely justifiable, but were communicated and implemented very poorly.
I think the issue was the activities escaped the subreddit and surfaced other places. Say you disagree with the Healthy at any Size crowd in the subreddit? Fine. Start harassing them on their Facebook pages, tumblers, etc and it was deemed (in my humble opinion) going too far.
The irony is not lost on me that to make Reddit a "safe place" for all some ended up booted off the site for activities outside the site itself. Same as the fact that the primary object of fph's disdain got far more attention and perhaps even sympathy than she would have otherwise.