That problem is not specific to SSL client certs. It potentially affects every authentication mechanism (on the same computer). Typing in your passwords? Keylogger. Using a password manager? Stolen passwords. The password database is encrypted and you have to type in a password to decrypt it? Keylogger.
If your system is rooted / infected with malware, you lost. The only solution is to format the drive and start over.
The alternative is to use a 2 factor authentication mechanism that uses a separate device, like your phone receiving a text message. That's a pain for the average user, and certainly not "simpler".
For everything else, there are much simpler solutions.