If you have a WordPress site installed in the parent directory (like /home) then you should be able to run my plugin in a browser by logging into the wp-admin of that site (the permission must allow that site’s user access to the subdirectories that contain the other sites). It may take a long time to scan all the other sites at once, depending on how many files there are and how fast your server is, so this method is usually discouraged. Also, my plugin adds some protection to the sites it is installed on but that does not protect the sub-sites. It is best to install the plugin on each site individually.
I am working on a CLI version of my plugin but it is not ready yet. I will let you know when I have something ready for testing.