Please note that version 2.3, fixing the issue that prevented the retention of WP class, is now live on WP:
http://wordpress.org/extend/plugins/navigation-menu-ids-classes/

And, as requested, GitHub:
https://github.com/aarontgrogg/wp-plugin-navigation-menu-ids-classes

Thanks to all above for the comments and patience while I got this revision together!

Atg