Thank you for your excellent and useful idea.
In order to get a performance boost, I keep my uploads directory in another location. The path and URL are specified on the options-misc.php page. It would be ideal if WP-MalWatch could use that information in order to find the uploads folder. As it is, the plugin sees that the uploads directory is not in its default location and just provides that error message.
Alternatively, could you please tell us how to modify the plugin code itself to hard-code in a different location for the uploads directory?