If I'm reading your link right, they are using user agents. Granted there's a lot. Maybe you could whitelist user agents you approve of? Or one of the commenters had a list that you could block. Nginx would be able to handle that.
If you try to rate-limit them, they'll just switch to other IPs all the time. If you try to block them by User Agent string, they'll just switch to a non-bot UA string (no, really). This is literally a DDoS on the entire internet.
In the hackernews comments for that geraspora link people discussed websites shutting down due to hosting costs, which may be attributed in part to the overly aggressive crawling. So maybe it's just a different form of DDOS than we're used to.