I don't think Thiel is naive enough to think that anything you can do with twenty people and two million dollars will "destroy" academia, but he does seem to have an agenda and the desire to prove a point.
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.
the spread of startup accelerators in the style of y combinator suggests that the entrepreneurship-as-education model is growing. not going to scale to everyone, but that's not the point. the point thiel's making is that entrepreneurs fare well without school, perhaps better, because when they're not in school taking instruction, they're in the world building things. if that's true, what's silly about it? if it's true that we're hampering entrepreneurship by keeping a special breed of human being tied up on class during 4 of their prime years, when we could accelerate entrepreneurship by giving them money to start things, then that's actually quite a profound mistake. so if thiel's project succeeds to the point where more such accelerators pop up, siphoning entrepreneurs out of school to achieve success without a degree, then he's made a profound point.