Prevent Multisite from creating sample page, sample post and sample comments

When you create a new site with multisite WP does not automatically change the context. So your action is added to the current site, not the new site. You have to switch first. Like this:

add_action ('wpmu_new_blog', 'wpse296303_delete_wordpress_defaults', 100, 1);

function wpse296303_delete_wordpress_defaults ($blog_id, $user_id, $domain, $path, $site_id, $meta) {
  // Switch to the newly created blog
  switch_to_blog ($blog_id);
  // Delete 'Hello World!' post
  wp_delete_post (1, true);
  // Delete 'Sample page' page
  wp_delete_post (2, true);
  // Delete 'Sample comment' page
  wp_delete_comment (1, true)
  }

I’m not sure if the ID of the default comment is 1, so you’d have to check that.