Now to address some concerns you specifically put forth in your post.

By nodes I assume you mean either economic agents or intelligent agents? Smart contracts for example can be intelligent agents, bots can be intelligent agents, and you can use a botnet to censor or suppress information so it's not a stretch to believe that intelligent agents can be used to promote a global moral regime which most of us disagree with.

One way to combat the nasty intelligent agents which we think could exist is to start building the friendly (friendly to our interests) intelligent agents today. First if you're familiar with extended mind theory then you'll understand that these intelligent agents will become a part of our minds. Our intentions will be encoded into them and our minds uploaded onto intelligent agents. For these reasons I would say this is about helping ethical people take control of their own mind and helping people to identify other people who share their ethics.

There is an argument to be made that these kinds of threats are merely transient states in a self-correcting system. If the economic >incentive to steal shiny cryptocoins generally erodes security, then security will improve and the problem will go away. If businesses >are being censored by DDoS attacks, at some point it becomes more economically viable to prevent the attacks; centralized websites >will tend toward decentralization, since it is significantly harder to DDoS and censor data in a highly redundant system — like IPFS. Will >people, by analogy, learn to become so personable as not to end up on the shortlist of an assassination market?

Assassination markets, decentralized ransom networks, it's all potentially going to exist. At the same time these sorts of networks already exist around the world but now with technologically improved communications. Not everyone agrees with warfare or wants warfare. Assassination markets would lead to warfare, and then there would be organized efforts to put an end to it. At this point in time, it is up to the early adopters and innovators to take on the responsibility of building protection mechanisms for future generations who might inherit a more decentralized world. For sure there are risks of terrorism, of war, but at the same time there is potential to build for peace.

Bitnation is an example of one of the first attempts at building a virtual nation. The virtual nation concept was birthed in many different places but I have independently contributed to one concept while Susanne independently came up with Bitnation. In both cases the idea is that as technology moves forward the concern of borders is going to diminish, it goes from geographical to digital. Virtual nations, tribes, communities, whatever you want to call the groups, in the end it is how people think which matters. People who think in ways compatible with how you think will be people you'll be more willing to work with, and by allowing people to voluntarily join virtual nations, or cyber tribes, or decentralized autonomous communities, you create order in cyberspace according to the rules and norms selected by individuals.

There will certainly be communities and groups who have agendas we don't like, who do things we don't like, and there will be individuals who have bad histories, and all of this will be flagged by the blockchain as well as by traditional law enforcement. The point here is to build the software necessary so like minded people can find each other and organize to solve problems.

Smart contracts, dispute resolution, reputation systems, sites like this, or concepts like what is being worked on by team Bitnation, are all about solving problems. The fact that we have these discussions means that at least some of us are giving it thought. One thing many of us early thinkers on the subject agree on is that a polystate or polycentric model is necessary for cyberspace. One order to rule them all, from the top down, is not likely going to work with the social norms we have in place and the attitudes of the people currently building the technology.

1. https://www.amazon.com/Polystate-Thought-Experiment-Distributed-Government-ebook/dp/B00IM5EM7W