First – about loading stuff from “mu-plugins”.
“mu-plugins” is a “must use” plugins folder. *php in there will load without the option to activate/deactivate like the usual plugins.
Further, “mu-plugins” folder does not look inside any folders. mu-plugins will load any *.php files but it will not open a folder unless there is a *.php file telling it too.
So a bit of trial and error is needed to install a plugin designed for the “plugins” in the “mu-plugins”.
Now let’s say I have a plugin folder inside the “mu-plugins” folder named “spam_tools”. I’ll still need a spam_tools.php file alongside the folder to tell WP to load the contents of the spam_tools folder:
<?php
$spam_tools = glob(dirname(__FILE__).'/spam_tools/*.php');
if( is_array( $spam_tools ) ) {
foreach ( $spam_tools as $spam_tool ) {
if( is_file( $spam_tool ) )
include_once( $spam_tool );
}
}
?>
Second, – restricting plugin menus to the SuperAdmin.
Since all that will just get a plugin loaded from the “mu-plugins”, you’ll still need to edit the plugin to keep its menus from appearing to any user but the SuperAdmin. Editing the role/cap is what I would try.
<?php add_menu_page( $page_title, $menu_title, $capability, $menu_slug, $function, $icon_url, $position ); ?>
The plugin author may add the menu page for users with “manage_options” $capability, it sounds like you want it to be “manage_network_options” instead.
If you want the menu to only appear in the Network Admin menus, that may need a bit of creativity as well, but it is certainly doable.