This appears to be fixed, as of at least rdiff-backup 1.2.8-1ubuntu2
Now there is --force required also before directories are written over.
andr...@stilgar:~$ rdiff-backup -r now temp/dest/ /tmp/
Fatal Error: Restore target /tmp already exists, specify --force to overwrite.
andr...@stilgar:~$
** Changed in: rdiff-backup (Ubuntu)
Status: New => Fix Released
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rdiff-backup well restore a file over the top of a directory without warning
https://bugs.launchpad.net/bugs/376454
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