That problem is not specific to SSL client certs. It potentially affects every authentication mechanism (on the same computer). Typing in your passwords? Keylog

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".