- Quit Safari
- Go to ~/Library/Safari/ in finder.
- Find “History.plist” file and edit it using textedit or text wrangler. (you may want to backup this file in case you messed it up)
- Search in the file for the URL (for e.g. yoursearch.com) or the text you are entering in the “top hits”.
- Identify the parent “<dict> …. http://yoursearch.com ….. </dict>” and delete it from the file.
- Find any other instances of the same and delete the entire “” tags.
- Start Safari and enjoy. “yoursearch.com” will no longer be there.
Worked for me in Safari 7.1.2.
Update: Unfortunately the top hit came back a little while later. I think it shows the top level of the site as a top hit if you visit any subpage a few times.