Problem solved
After updating the system, I found that the aforementioned vulnerability in Safari is gone. Now the download manager is able to decipher the altered script files and warn that the package may contain an application. Since you know you are downloading a media file, this warning is enough to raise your alert that something fishy is going on.
The turnaround time of the fix is fast enough, which is a good sign that Apple is taking Mac security seriously. If your system has not been patched, you can download and install the update using the Mac's built-in Software Update, or get it from this link.