A script to be used with WP-CLI's `wp eval-file` to remove super-admins from all sub-sites in a network (except the primary site in the network when applicable).

remove-super-admins.php

<?php
// Fetch all superadmins on a site.
$super_admins = get_super_admins();

// Loop over all super admins
foreach ( $super_admins as $admin_slug ) {
	// Get a user object for this user.
	$user = get_user_by( 'slug', $admin_slug );
	
	// Fail-safe, maybe the slug somehow couldn't be identified.
	if ( ! $user ) {
		echo "Could not find the user object for `" . $admin_slug . "`\n";
		
		continue;
	}
	
	echo "Processing the user `" . $admin_slug . "` (user id: " . $user->ID . ")\n";
	
	// Get all sites for this user.
	$sites = get_blogs_of_user( $user->ID, true );
	
	// Loop over the users sites.
	foreach ( $sites as $site ) {
		$site_id = $site->userblog_id;
		
		/*
		 * Skip the main site in the network, for consistency.
		 * Not neccesarely required, a network admin will exist even if removed from all sites,
		 * but it makes a more consistent admin UI experience for many.
		 */
		if ( $site_id === get_main_site_id() ) {
			continue;
		}
		
		// Check that the user has no posts on this site, or else content could be lost.
		$posts = get_posts( array(
			'posts_per_page' => 1, // We only need a single post to know this user has content that needs moved.
			'author'         => $user->ID,
			'post_type'      => 'any', // We use WordPress' keyword `any` to mean any post type that may exist as a catchall.
			'post_status'    => array( 'publish', 'pending', 'draft', 'future', 'private', 'inherit' ), // There are more post stati, but these are the known ones that represent "real" content.
		) );
		
		// If posts are found, do not remove this user.
		if ( ! empty( $posts ) ) {
			echo "Site " . $site->siteurl . " (#" . $site_id . ") has content by the author `" . $admin_slug . "`\n";
			continue;
		}
		
		
		// Remove the user from this site (aka "blog" in WordPress).
		$remove = remove_user_from_blog( $user->ID, $site_id );
		
		if ( is_wp_error( $remove ) ) {
			echo "Error when removing user from site #" . $site_id . ": " . $remove->get_error_message() . "\n";
		}
		
		// The `remove_user_from_blog` function returns a boolean `true` if it was successful, this is just a nice to have section.
		if ( true !== $remove ) {
			echo "Something went wrong, and we could not remove the user from the site " . $site->siteurl . " (#" . $site_id . ")`\n";
			
			continue;
		}
		
		// Clear the cache for this site.
		wp_cache_delete( $site_id . '_user_count', 'blog-details' );
	}
	
	// Clear the user cache when done, it's nice to be tidy.
	clean_user_cache( $user->ID );
	
	echo "Done processing this user...\n";
}

echo "-----\n";
echo "Finished removing super-admins from sub-sites in the network.\n";