When disabling in a plugin you’re creating, you need to call it from something like the admin_init() hook (rather than just in the content of the main plugin file), ie:
// Remove the pointer scripts
function my_remove_pointer_scripts() {
remove_action( 'admin_enqueue_scripts', array( 'WP_Internal_Pointers', 'enqueue_scripts' ) );
}
add_action('admin_init', 'my_remove_pointer_scripts');
Otherwise I’m guessing the add_action() in template.php is getting called after you try to remove it, thus not working as you’d hoped.