I know this post is pretty old, but because I came across the same issue and this post came up higher than one with a solution, I figured I’d add this, which worked for me.
Source: http://coffeecupweb.com/how-to-exclude-or-hide-categories-from-category-widget-in-wordpress-sidebar/
//Hide categories from WordPress category widget
function exclude_widget_categories($args){
$exclude = "1,4,8,57,80";
$args["exclude"] = $exclude;
return $args;
}
add_filter("widget_categories_args","exclude_widget_categories");