Alright- I've figured it out. I'm not even remotely bright, but here is the problem:

The reason that autocomplete keeps filling in the websites and bringing it up as a "top hit" and suggesting things is because you have a link to that site saved in your bookmark folder.

STEP 1: DELETE ALL THE SITES FROM YOUR BOOKMARK FOLDER THAT YOU DO NOT WANT TO SHOW UP IN AUTOCOMPLETE.

STEP 2: Clear all history, restart Safari, and WALLA- Autocomplete shows NOTHING.

YAY!!!!

Alright- I've figured it out. I'm not even remotely bright, but here is the problem:

The reason that autocomplete keeps filling in the websites and bringing it up as a "top hit" and suggesting things is because you have a link to that site saved in your bookmark folder.

Step 1: Delete all the sites from your bookmark folder that you do not want to show up in autocomplete.

Step 2: Clear all history, restart Safari, and Voilà - Autocomplete shows nothing.