We're using MySQL as well (5.1), but I also do not use MySQL Workbench. Instead, I set up a batch file and use a scheduled task to do unattended nightly full dumps, using the delivered MySQL command-line tools. I can then use the resulting dump file to completely rebuild the databases as needed. I also periodically refresh the development site's mojoportal database using these. The main command for a command-line export is:
mysqldump --user=root --password=___ --log-error=errors.txt --single_transaction --add-drop-database --databases mysql mojoportal > fulldump.sql
If you then want to rebuild the mojoportal and MySQL databases from the export:
mysql --user=root --password=___ mysql < export_file
mysql --user=root --password=___ mojoportal < export_file
The rest of the batch file is just to save a rotating set of export files, and report errors. I can post the full batch file if you'd find it helpful.