You should just start with a new install and import the existing site into the new install.
Starting with an existing install triggers that warning but if you start fresh you can setup the subfolder structure.
You can add this to functions.php to allow a subfolder install in multisite:
add_filter( 'allow_subdirectory_install',
create_function( '', 'return true;' )
);
Untested by me, use at your own risk (test server), and let me know how it works! I am recommending new install and migration as a cleaner solution. Duplicator is pretty simple to import your content.