I have a similiar problem. MU-sites with jetpack activated went offline, after renaming the plugindir and thereby deactivating it, i get this when I want to reactivate:
Notice: wpdb::escape is deprecated since version 3.6! Use wpdb::prepare() or esc_sql() instead. in /wp-includes/functions.php on line 2905 Warning: require_once(wp-content/plugins/jetpack/modules/publicize/publicize.php): failed to open stream: No such file or directory in wp-content/plugins/jetpack/modules/publicize.php on line 26 Fatal error: require_once(): Failed opening required 'wp-content/plugins/jetpack/modules/publicize/publicize.php' (include_path='.:/usr/share/pear:/usr/share/php') in /wp-content/plugins/jetpack/modules/publicize.php on line 26
Note: I remove the first part of the absolute path.