Add to customizations plugin, not including the top 4 lines, or create a folder in your plugins directory and add this file, then activate the plugin in your dashboard.

pmpro-admin-only-profile-edit.php

<?php
/**
 * Plugin Name: PMPro Admin Only Member Directory Profile
 * Description: Remove area in profile with checkbox to show profile in PMPro Directory, and add back the functionality only for administrators.
 */

add_action( 'init', 'pmpromd_remove_profile_field_action' );
function pmpromd_remove_profile_field_action() {
	remove_action( 'show_user_profile', 'pmpromd_show_extra_profile_fields' );
	remove_action( 'edit_user_profile', 'pmpromd_show_extra_profile_fields' );
}
add_action( 'show_user_profile', 'pmpromd_show_admin_only_profile_fields' );
add_action( 'edit_user_profile', 'pmpromd_show_admin_only_profile_fields' );

// show the option to hide from directory on edit user profile
function pmpromd_show_admin_only_profile_fields( $user ) {
	global $pmpro_pages;
	if ( current_user_can( 'manage_options' ) ) {
		?>
	<h3><?php echo get_the_title( $pmpro_pages['directory'] ); ?></h3>
	<table class="form-table"> 
		<tbody>
			<tr class="user-hide-directory-wrap">
				<th scope="row"></th>
				<td>
					<label for="hide_directory">
						<input name="hide_directory" type="checkbox" id="hide_directory" <?php checked( get_user_meta( $user->ID, 'pmpromd_hide_directory', true ), 1 ); ?> value="1"><?php printf( __( 'Hide from %s?','pmpromd' ), get_the_title( $pmpro_pages['directory'] ) ); ?>
					</label>
				</td>
			</tr>
		</tbody>
	</table>
		<?php
	}
}