That is true, I don't really know what the answer is. You could do something like show half code/half readme, with extra code hidden behind a fold.. but I'm sure that would annoy devs working on those additional hidden files.
I'd be happy with a README-first design that had a link to move the README below the code, and that remembered which one you want on top for each repository. (Along with a preference for logged-in users to decide what they want.)
