Ivan,
You were so close! The problem was exactly what you described, that the Javascript we try to insert was messing up the AJAX response from JomComment.
I modified the following 2 files as below, and comments are now appearing in my Facebook stream and on the site itself:
/com_jomcomment/main.jomcomment.php, update the jfbcLibrary call to NOT load the Javascript:
$fbClient = JFBConnectFacebookLibrary::getInstance(false);
/com_jfbconnect/libraries/facebook.php
Made minor modifications to the getInstance and constructor calls. These changes were pretty much already there, just commented.
With that, it seems to work. Please test, and let us know what results you have!