The simple way to have your files encrypted on disk is to create an encrypted filesysytem, such as
TrueCrypt and other
similar options. This is transparent to Wowza as it happens at the OS level.
Alternatively another simple option may be to apply a hash to the recorded assets thus making them un-streamable unless you unhashed the files with your secret key.
You mention that you don't require that these files are made available for streaming, and so a simple extension to the above is to move them out of the streaming directory that Wowza uses. We provide
example frameworks for this to move the recordings outside of the StorageDir content directory which will prevent them ever being able to be streamed, encrypted or not.
These are tools outside of Wowza that can be used for many purposes, but if it is to create unplayable streams, then unless they are decrypted (and optionally moved to the StorageDir content directory) then they should be quite safe.