Widget settings are not tied to a theme, but to a sidebar. If the sidebars have the same name/id in each theme then widgets will stay the same. Changing the sidebar names for each theme will allow you to have different settings for each without affecting the other.
Then use this:
http://wpmu.org/how-to-test-new-wordpress-wpmu-or-buddypress-themes-in-a-live-environment/
When you are ready for A/B testing you can use our plugin that you referred to.