The "problem" that the whole distributed paradigm brings to communities is the same as its greatest strength: if nobody controls the system, then anyone has just as much influence as their peers. This means that systems will have to be put in place to give some power over others in order to control the community.
This is where I believe the crux of the issue lies: in the distribution of power.
If anyone can decrease someone's federated reputation, then so can the trolls.
If you require people to "join" a community, whether by participation or time or other means, trolls will do that as well if it is easy to do so.
If I were trying to create a community of people who are at a higher risk of being harassed I would have my community structure take some cues from HN, Reddit, and the like.
One of the things I love about HN is that you need a certain amount of rep to downvote. This alone eliminates a lot of the issues Reddit has where everything turns into mob rule as everyone, including community outsiders, have the ability to influence discourse. Going one step further, I would propose an invite system. While an invite system would mean slower growth initially, we're trying to optimize for quality in the community, not quantity.
I had some alarms go off in my mind while reading this article's seemingly nonchalant approach to what is effectively censorship, but in a distributed system I guess this is of no concern as everyone can just "fork" the community and start their own.