Are you implying that it's stupid to keep SSH keys in one's home dir?
Your SSH key should only exist on your desktop/laptop, never on a server. Use ssh-agent (and agent forwarding, when needed), which was designed for this.
The best approach is to use yubikeys and pkcs11 along with your ssh-agent so the private key never exists on disk at all, but at the very least, using vanilla ssh-agent is an imperative.
Yes, such enterprises are stuck in the 1980s and deserve what they get.
(Also, "personal files" shouldn't mean SSH private keys in any stretch of the definition.)
While the more secure organisations disable USB in the OS / BIOS and glue the ports shut to prevent anyone using them, to prevent against data loss by employee.
Source: worked in two different organisations that literally glued the USB ports shut.
Does not necessarily help when the machine is compromised. Using one key per machine and storing it in the corresponding home directory seems safer to me.
If the keys are in a thumbdrive and in a keyring, you can only attack two things: 1) the user namespace, 2) the thumbdrive's mounted contents while it is inserted _and unlocked_. This limits the scope of attacks. When the keys in the keyring expire ("-t life" option to ssh-agent), you can't even attack that.
