I used to rely on the trick below, not sure if it still holds true. I don't use Safari anymore.
Open the Bookmarks window (Bookmarks: Show All Bookmarks), put the you want to alphabetize into a folder, and then drag that folder into the Finder. The Finder alphabetizes the bookmarks; you can then just drag the folder back into the Bookmarks window. You probably have to set the Finder to arrange files by name before it will work.
Note: when you drag the folder back, you'll now have two folders, the original and the sorted one. Just delete the original, and you're set.