Disallow Jetpack modules.

blacklist-jetpack-modules.php

<?php
/**
 * Blacklist Jetpack modules.
 */
function blacklist_jetpack_modules( $modules ){
    $jp_mods_to_disable = array(
        'contact-form',
        'shortlinks',
    );

    foreach ( $jp_mods_to_disable as $mod ) {
        if ( isset( $modules[$mod] ) ) {
            unset( $modules[$mod] );
        }
    }

    return $modules;
}
add_filter( 'jetpack_get_available_modules', 'blacklist_jetpack_modules' );