Thanks all,
Just don't allow it to happen. Treat your backups as precious data.
While I'm old fashioned and would dig a hole in my garden and bury them in a safe, insurance requirements state we need to store our backups offsite. We do not have a second location so we are using a third party (who are very reputable), even so, we have some sceptical sorts who want every eventuality covered.
Perhaps preaching a little trust in your fellow man may be the way to go!

It is technically possible to encrypt backups, but in many cases doing so greatly increases the probability of data loss, which sorta defeats the purpose, doesn't it?
Having had this difficulty in the past with restoring backups to different base systems, this is a good point, but if the trade off between security and reliability is an accepted risk by the admin/management then it would be nice to have the choice. It is also a feature of various other backup software I have come in to contact with in the past.
I assume this would be part of the file system that you are backing up to... ie a share on the network would use an encrypted file system
Thanks Janet, I will give this solution some thought and post back how we decide to move forward (if at all).
This contrib does the MySQL dbs only.. http://wiki.contribs.org/AutoMysqlBackup its not a part of the sme server backup system.
and thanks Terry, this was the one thing I had come across, although, as you rightly mention not a complete solution. For us the files are more critical.
One option may be to use a zero knowledge cloud offering such as Tresorit or SpiderOak and omit the files from the physical backups...
Comments welcome, thanks again.