Look for the images_from_wpgallery function within the WPSupersized.php file. Within that function you’ll see a get_children array
Exclude the get_post_thumbnail_id() at the end of the array, i.e.:
$images = get_children(array( // gets images attached to the post/page
'post_parent' => $postid,
'post_type' => 'attachment',
'numberposts' => -1, // show all
'post_status' => null,
'post_mime_type' => 'image',
'exclude' => get_post_thumbnail_id(),
));
This worked for me.