Sorry for the slow response. Here is the process for deleting out old config controllers and keeping the table size to a minimum. I have run this successfully from terminal and have it set up to run through cron tonight and will post if there are any problems.
I created a script which I have saved as controllers.sh. This is just a simple file with the following script:
mysql -u YOURDATABASEUSERHERE -pYOURPASSWORDHERE moodle <<EOF
DELETE FROM mdl_backup_controllers WHERE timecreated< unix_timestamp(now() - interval 7 day)
Put in your database username after the -u and your database password after -p (no space here).
If your database is not called moodle, then change this to the appropriate name. This will delete out all controllers over a week old.
I have then made the following entry to crontab:
00 01 * * * bash /home/moodle/Desktop/controllers.sh
This should run the script nightly, though I have had issues with bash scripts through cron before so will post tomorrow if it does not run as expected. This is the direct path to where I put the script file - you will obviously need to direct it to wherever your script file is.