malware could just capture that

From the article:

This means that while a keylogger might require admin access to install, any app or script with sufficient permissions could access these plaintext keys.

Malware to capture input would require privilege escalation as well, whereas this just requires being able to run code/copy files.

there is not a simple solution

But there are:

• use the system keyring
• store unencrypted key in memory in a background process (I.e. DIY keyring)

Essentially, force malware to either copy keystrokes or memory, both of which require admin privileges on most systems.