This behavior is unconscionable when there is such an obviously trivial technical solution to this problem.

Here is my quick and dirty technical solution.

(1) Place a restriction: only allow users who have uploaded a given file to download that file. In essence, keep an "uploaded" flag for each file/user.

(2) Challenge-response to validate local copy of a globally-known file: To continue receiving the benefits of de-dup, don't actually upload an already globally-known file, but perform a challenge-response with the client on the contents of the actual file. This will still leverage most of the benefits of de-dup w.r.t bandwidth savings.