These directories can indeed be safely removed.

On Ubuntu and other non-rpm-based systems, rpm is typically used to
build and inspect RPM packages, not to install them or manage a
database. The problem for non-rpm-based systems is that the rpm tool
cannot (currently) operate on package files without accessing its
database. If the rpmdb doesn't exist, you get a nasty warning (that
calls itself an error) with every command:

$ rpm -qp fedora-release-18-0.8.noarch.rpm 
error: cannot open Packages database in /var/lib/rpm
fedora-release-18-0.8.noarch

The fix for Debian and Ubuntu was to configure rpm such that it creates
a database in $HOME/.rpmdb, since $HOME should normally be writable. See
http://bugs.debian.org/551669.

If you want to prevent these directories from being created, you could
try to figure out what process is running rpm with HOME set to null or
/. I agree with #3, it sounds like cron.

Bottom line, I'm not sure what the bug is here. A lot of Linux commands
and applications generate configuration files or directories as a side
effect of running, and if you run them as root without a HOME, you'll
get the same effect.

** Bug watch added: Debian Bug tracker #551669
   http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=551669

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https://bugs.launchpad.net/bugs/1069350

Title:
  suspicious /.rpmdb root directory

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