Just delete the content of your plugin directory using subversion in the SVN repository.
svn co http://plugins.svn.wordpress.org/your-plugin your-plugin
In other words, these instructions may help you update the plugin files.
svn status
svn update
svn commit -m "Emptied my plugins..."
If you need to delete files use this
svn st | grep '^!' | awk '{print $2}' | xargs svn delete --force
I think you will also need to send an email to plugins at wordpress.org, but they occasionally remove empty directories.
When I first wrote to this email address the great Otto replied. Enjoy.