A bit late to the party guys, but I just needed to do this myself. A workaround would be via SQL queries in phpmyadmin, something like:
IN ( SELECT `term_taxonomy_id`
WHERE `taxonomy` = 'category' )
GROUP BY `object_id`
HAVING ( COUNT( `object_id` ) >1 )
(replace wp_ prefix with your prefix)
Usually "uncategorized" has a term_taxonomy_id = 1. The above query would group all the post ids where there is more than one category, so naturally "uncategorized" is displayed first in the grouping. So select all those rows that have a term_taxonomy_id = 1 and delete them. And that's about it!
Now all you have to do is edit the count field of "uncategorized" (term_taxonomy_id = 1) in the wp_term_taxonomy table. Count number is how many articles are listed in this category, but the specific field is not updated automatically.
If you go to your wp admin panel, categories section, the old (wrong) count number is still displayed, but if you press that number and go to the posts list of 'uncategorized', wordpress usually recounts the posts that are affiliated with that category. A correct count will be displayed on your top right, so go then into your db, and edit the count field accordingly :)
Edit: Actually, the count does get eventually updated, just not right away, so you may want to skip the manual count update.