i know that issue. It's probably one of "those-who-must-not-be-talked-about" ;-) I think, you cannot do this by read-rules, as these usually refer to the objects. As soon as you disallow read access to these objects, they will not be shown in the articles...
My suggestion: you should try to override the full-view-templates of the folder class, the image class and the file class IN the media section only (override condition: "section=media")
Besides marking as invisible the Media folder, which would not work as all its children would be hidden too, you can simply set it to a "reserved" section, that is not visible to anon user (ie. he has no content/read access to that section). You then switch back to the "media" section to all children of media, and you should be done
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