There's no way to directly edit that list. It's unclear how it would clear it out since it's just using folders you've used before and it may be hard to tell which ones you may or may not want quick access to again.
If it's that big of a deal, you may want to look into why you have so many destination folders. If, for instance, many of the folders are all underneath a common folder, you can also try separating things out by having Hazel move to a base folder, then have Hazel monitor that folder and then sort it to its final place.