This is and has been my only major complaint with Geeklog. After days of fighting with Drupal, I figured it would be easier to mod Geeklog. I would classify this as an ugly hack though (and it require updates with every patch).
My fix: Set the sid value to the ideal "TitleOfArticle" and ...
RewriteRule ^topic/(.*) index.php?topic=$1
RewriteRule ^article/(.*) article.php?story=$1
Then a massive search and replace on php files:
article.php?story= --> article/
index.php?topic= --> topic/
http://www.site.com/index.php?topic=GeekLog becomes http://www.site.com/topic/GeekLog
http://www.site.com/article.php/20060918174323100 becomes http://www.site.com/article/sid_text
An elegant solution for this build into Geeklog 2 would be ideal!