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.