Hey,
To be honest I don't know a clever solution to sort the categories/sub categories too. You can modify template-portfolio.php and change the category array order but it requires manual work/coding for each category. You need to find following line:
$categories = get_categories($args);
Then you can rearrange the positions with following code:
$categories = get_categories($args);
$customcats = array();
//change category position
$customcats[0] = $categories[1];
$customcats[1] = $categories[0];
$categories = $customcats;
I.e. the code above would swap the category position (the second category moves to the first place and the first category goes to the 2nd place). But the problem is that this will only work for one portfolio page. If you'd like to change the order on different pages you'd need to work with is_page(), etc. conditional tags too: http://codex.wordpress.org/Conditional_Tags
I'd try to get the plugin to work with subcategories instead :)