>The attacker put an SSH key on the box, which was unfortunately exposed to the internet via a high-numbered SSH port for ease of admin by remote users, and placed a trap which waited for any user to SSH into the jenkins user, which would then hijack any available forwarded SSH keys to try to add the attacker’s SSH key

You could also fund/donate to/advocate for a better SSH agent.

I use both Pageant and ssh-agent in my home network for ease of ssh'ing into boxes, especially Unifi gear and some dev VMs. I don't think I will stop using agents, but I probably wouldn't use them at work.

Why couldn't there be an agent that required you to touch a Yubikey before it'd allow keys to be forwarded? Why couldn't you add prompting and timeouts to an agent?