So assume you just uploaded the certificate you use to identify yourself to the MySQL server to Github or some other place it doesn't belong...and there is no undelete.
First: Don't panic.
Often a password is required besides a certificate to connect to the server. So someone with the certificate can't use it without the password. The certificate itself might be protected by a password, but that's really rare. Also access to MySQL and/or your account should be limited to certain IP's.
The next step is to revoke the certificate. This is possible since MySQL 5.6.3 by using a Certificate Revocation List (CRL).
A CRL is a list of the serials of the revoked certificates and signed by the CA. So this will only work if the certificates have unique serials.
To get the serial of a certificate with OpenSSL:
$ openssl x509 -in client-cert.pem -noout -text | grep 'Serial Number'
Serial Number: 3 (0x3)
To get the serial of a certificate with GnuTLS:
$ certtool --certificate-info --infile client-cert.pem | grep 'Serial Number'
Serial Number (hex): 03
If all certificates have the same serial, then you can't revoke them and you have to create a new CA and all other certificates.
If you do have unique serials for your certificates then you can use GnuTLS to create the CRL:
$ certtool --generate-crl --load-ca-privkey=CAkey.pem \
Then you will be asked in how many days the next CRL will be issued and what the CRL number is.
With OpenSSL you can use the 'ca' command with the -gencrl option, but that requires a bit of a setup.
If you have the CRL file then you can use --ssl-crl option for the server and clients to let them know which certificates are revoked. It looks like MySQL Workbench can't be configured to use CRL's, but it should work for most other tools and connectors.
The major drawback of using a CRL is that you have to update the file for all servers and clients if you revoke a certificate.
With OpenSSL you can use openssl crl -in CAcrl.pem -noout -text to view the CRL contents and with GnuTLS you can use certtool --infile=CAcrl.pem --crl-info
If you use a public CA for your MySQL certificates then the CA can revoke the certificate, but then you still need to get the latest CRL from your CA and distribute it to all servers and clients. This is because MySQL doesn't fetch the CRL from the 'CRL Distribution Points' URL's which may be embedded in the certificates.