Bookmark Sorter lets you:

• Alphabetically sort your Safari bookmarks.
• Put folders above bookmarks.
• Rename bookmarks that have the same name.
• Remove duplicate bookmarks.
• Without having to shut down Safari.

While:

• Keeping the order of your buttons in the bookmarks bar as is.
• Keeping your bookmarks backed up.
• Automatically keep your bookmarks sorted according to your preferences.