The author points to the behavior as a "flaw", but I disagree. There's no defect or bug in the software, it's an architectural design. It would be a flaw if Dropbox claimed that each user's data was individually encrypted with a private key tied to the user's account credentials, but I don't think that claim was made. I, for one, think that the deduplication is actually a huge benefit, saving time and bandwidth in unnecessarily uploading files.

As the author suggested, the only way to ever ensure that you're files are inaccessible to anyone but yourself is to encrypt them locally with something like EncFS or TrueCrypt.