The HTML cleaning is controlled by the saf/lib/HTML/Messy.php package. span is one of the tags listed in the $messy->stripTags list. To stop it from being stripped out, simply remove it from the list, either in the class itself or in the code that calls it (which, through Xed, would be inc/app/xed/lib/Cleaners.php and inc/app/xed/lib/Widget/Xeditor.php).