Is it possible to serve a theme from outside the web root?
If you have

Options +FollowSymLinks


set for the DocumentRoot for your Drupal site, you can put the proprietary theme anywhere you want as long as you create a symlink to it somewhere Drupal searches for themes (eg, sites/all/themes).

Just keep in mind that Apache needs to be able to read it.  Whether the client can read it directly is a permission issue, but if Apache can read it a savy client can get it via custom PHP.