> The idea of freedom in (fundamental) research seems long dead
Is it so in the US? Or where? Here in Russia it is far from true, at least in the top institutes. As long as you produce publishable results, you may do virtually whatever you want, and nowadays pretty much anything is publishable. And this way you get funding, too, because the funding agency doesn't seem to want you to solve some particular problem, it just wants to be sure your science keeps up with the world.
The downside here is that the academy usually pays bad. Thus it seems most successful labs work like 70/30 on commercial projects and "pure science". Anyway, when you work on commercial projects you usually get much more interesting results than you'd care to publish.