I hope you're not implying that the point of the Fellowship is to destroy academia.
The point, however, is silly. Cherrypick the twenty brightest students you can find, give 'em a bunch of money and all the connections that come from having Peter Thiel invested in your success, and I'm sure that a lot of 'em will do well. But that doesn't scale.
Thiel is definitely pro "different" from the current system.
I think the idea of promoting more entrepreneurial activities earlier is great, but it seems very anti-university/higher ed in his vision rather than as an alternative path.