Not mentioned in the article, but if you add the key to your agent with "ssh-add -c <key>", then whenever the key is used to connect to another machine by the agent, the agent will prompt (on the machine where it was initially run) to confirm that the connection is intended, generally via "ssh-askpass".

In my world, I use this routinely, precisely to detect a connection using a hijacked session, as described in the article. It does not detect the agent hijacking itself, it only detects new connections -- it pops up for all connections, both intended and unintended.

I know we're all supposed to do defense in depth, but I confess to having a bit of a jaundiced view of attacks that begin, "first, become root on a machine in the target domain....". Containment is a good idea, but if you're at the point where you're doing containment of compromised root accounts "inside", things have gone pretty far wrong already.