I think the solution to this problem probably doesn't involve trying to track down these bad nodes. Rather, more people should host Tor nodes, so as to reduce the chance of someone connecting to a bad one. As big as intelligence agencies are, they cannot operate too many nodes easily - the more nodes they operate, the bigger the chance that someone notices suspicious activity going on. On the other hand, there are a lot more civilians who can host Tor nodes
without it being suspicious, thus dealing with the threat of intelligence agencies.
I'm curious about what the exact ratios would be, if there were a way to find this out (probably not).