Not sure you rec'd Shield Security, but I just noticed that the Shield Security plugin has 2FA capability within the ‘Login Guard' section. It would seem to me that that could work for implementing 2FA on any website. It SOUNDS like it would work well with LifterLMS to control the ‘Student' user type.
Does this make sense?
This might be more of a “Hey, can you look into Shield Security by iControlWP?” It seems pretty robust, highly rated, and 80,000 installations (although not as many as iThemes with 900,000).