Looking at the original study:
These were intro stats classes with 100-1000. These classes are already basically a teacher lecturing, minimum engagement, simple material, no ability to have complex homework, and from the looks of things not in the student's major specialization (so super 'in-depth' learning is unnecessary)
Universities have realized for years that they are not very good at these types of classes. They've tried to move these courses online or encourage students to take these at community colleges. But, you don't (or shouldn't) go to university for these classes, you go to the university for the more specialized upper division training in your department. I would be more interested to see if a high level, small, for majors course could be replaced by a similar program. It's worth noting the even the Khan Academy classes are still the 'factory' classes, he has very few 'specialized' classes in more complicated subjects.