You definitely need to do some work on this plugin.
I used it to get rid of my redundant media files but it also deleted a bunch of CSS, ZIP and other clearly non-media files.
Lucky I've got a full backup so I could restore the files... and lucky your plugin is Open Source, otherwise you might end up with a massive lawsuit for damaging peoples' data.
My suggestion is that you "teach" the plugin to recognise file types. It's not that difficult in PHP.
This plugin can only be used if your uploads folder doesn't contain important data, otherwise don't even think about using this plugin.