If a user is following another user around and commenting on everything they do, the solution there is to ban a user, not a subreddit.
A good analogy is this: If there's a hole in your tire, you patch it up. But if there's always holes forming in your tire, you have to throw out the tire.
FatPeopleHate wasn't just offensive to some people, it was objectively out of control. First off, the core idea of Reddit is not absolute free speech, but the libertarian principle of absolute sovereignty over one's property, which in their case means the right of any community on the site to have absolute sovereignty over their own subreddit, free from interference by both the admins and by the other users.
FPH was constantly bullying people and brigading in other subs (GTAV, Fitness, loseit, even SuicideWatch at one point) and interfering with the culture and functioning of those communities. The problem was too big to solve by banning a few people. When they targeted the admins of imgur, with the encouragement of the mods no less, that was the last straw.