Cron job has the following as it's last steps:
Deleting old draft files... done.
Deleting orphaned preview files... done.
Cleaning up files from deleted contexts... done.
Deleting trash files... done.
Would temp turn off automated backups if on and attempt running of the cron job via command line to see if those don't 'automagically' disappear. Unfortunately, there is no command line script to empty the trash or search for orphaned files. But, maybe by inspecting the cron jobs one could get a leg up on creating a script.
Also, check moodledata/temp/backup/ for in-complete backups. There might be many. From my experience, it's safe to manually delete the contents of that directory - or one could move contents out to a holding area if unsure. That might free up some space for ya!
'spirit of sharing', Ken