mysql workbench connection type tcp/ip over ssh with libpam-google-authenticator enabled
You can still use Google Authenticator with mysql workbench, but you will need to change how SSH and Google Authenticator work together.  When you login via SSH, you probably enter your password and then you are prompted for your Two-Factor pin.  You want to change this so that you enter your password and pin, one directly after the other, on one line as the password: 

[my-password][two-factor-pin]

This will work with MySQL Workbench TCP/IP over SSH.  I modify /etc/pam.d/sshd to use the forward_pass option for the Google Authenticator module.  You will need to put a line like this at the top of /etc/pam.d/sshd:

auth required pam_google_authenticator.so nullok forward_pass

Google Authenticator will authenticate the pin, strip it from the password, and pass the password along to the other PAM modules.