Managing WordPress with SVN, need help…

I opened a similar discussion on this topic in a separate forum here on WordPress, but I never got any useful feedback so I thought I’d rephrase my question and post it here.

I am using SVN to manage my client’s sites built with WordPress. It works perfectly until I run svn commit in the remote working copy. (In case that’s not the best terminology I mean when I run svn commit in the live site (so public_html, www, or whatever the folder is), when I do this if the client has deleted a photo from their media library, or a plugin, that was previously added and committed to SVN then I get an error from SVN like this:

svn: Commit failed (details follow):
svn: Directory '/path/to/remote-working-copy/wp-content/plugins/my-page-order/.svn' containing working copy admin area is missing

This is obviously because that plugin or file wasn’t deleted using an SVN command, so I’m wondering if anyone has any ideas on how to overcome this obstacle beside disabling the clients ability to delete media files or plugins.

Note: Though I haven’t run an update of the WordPress core from WordPress I suspect I will encounter this same issue when I have to upgrade.

Thanks!