We seem to have worked through this issue by adding the Subclipse plug-in (
http://subclipse.tigris.org/) to the Audium 5.2 environment. This stopped the behavior of the pages\.svn directory from getting blown away.
I had tried just adding the .svn to the team/Ignored Resources preference but that didn't help. It seems the Audium 5.2 plug-in really need Subclipse to ignore the directory.
Caveat, we aren't generally using Subclipse from within Audium as part of our processes. The directories remain checked out and we do commit/update from either the Tortise shell extension or from the svn command line in a dos window. As such, I can't promise what will happen if you use Subversion via the Subclipse console.