These are well known attacks. In case of Freedom Hosting this maybe was the cause for finding the server. Mitigation exists. Today big illegal darknet websites run lots of Tor servers on their own. You can also manually set trusted guards or other nodes in the chain so no malicious node will ever be part of your path through the network.
Yes, if you manually and wisely choose your own guard nodes, then you can avoid these attacks. You should be sure that those guards can't themselves be linked to you, either.
