@rythmdoctor, I also needed this functionality. I had already written a function to remove unwanted categories from any get_the_category result, so I was able to add just one line to Yoast's plugin.
Put the following code in your functions.php. Change 30,31,32 to the ID(s) you wish to exclude.
function get_the_category_exclusions($categories) {
$args = array(
'categories' => $categories,
'exclude' => '30,31,32'
);
return exclude_categories($args);
}
function exclude_categories($args) {
$count = 0;
foreach ($args['categories'] as $category) {
if(strpos($args['exclude'],$category->cat_ID)){
unset($args['categories'][$count]);
}
$count++;
}
$categories = $args['categories'];
return array_values($categories);
}
Then on yoast-breadcrumbs.php add the following after $cats = get_the_category(); (approx line:232).
$cats = get_the_category_exclusions($cats);
This solution is tested and working for WP v2.8.4 Plugin v0.8.4