If you think MU is the victim here and that the FBI are the criminals, you’ve got it backwards. They took down individual links only, while still keeping the infringing files on the server, and all the other un-reported links to that exact file (they also hashed each upload, so to detect duplicates, and complete the upload instantly and have 1 data file... a fingerprint system they never used to prevent re-uploads of…
Removing individual links makes sense--if someone filed a DMCA request with Dropbox for a song and it ended up getting removed from my Dropbox as well that would be ridiculous. In the case of something that is always illegal (say child porn) there would be a duty to remove all instances of a file, but when it's a case by case basis of whether or not there is a copyright issue it does not make sense to take files down…
Dropbox has a very clear concept of private files and public files. If a DMCA request was issued for a file you're storing in your public folder, I would certainly expect Dropbox to remove all instances of that file in all public folders on all accounts.