I'm not quite so interested in the hypocrisy part, but as a Thiel fellow working on a pretty research heavy project (in biomedical tech), the academia + industry interplay is quite interesting.
For me, the fellowship has been anything but a way to abandon academia; indeed, my project depends heavily on collaborations I maintain with folks in the academic world, not to speak of my curiosity there. Thus, while the fellowship enables me to wear an industrial hat for the present, I see it as an interaction with a slightly different facet of academia. I've temporarily put down my classes to study the translational part of science, and hopefully help move it along.
So, for me the fellowship doesn't undermine the advanced research society needs, but enables it in another way.