I was able to achieve this! I modified the extension to do so. In the file content_script.js I added the following code to execute right before the page is parsed:
$('a[href*="callto"]').each( function() {
var link = $(this), newUrl = link.attr('href').replace(/^callto:/,'sip:'), phoneNumber = newUrl.replace(/sip:/, '');
link.attr('href', newUrl);
link.attr('rel', phoneNumber);
link.addClass('fop2-click-to-call');
});
It would be great if you can add this to the extension so I don't have to modify it every time I update. But if not, it's fine too!