What other files belong in the root site folder?
The simple answer is: none. The public files folder is an area Drupal uses to store files. It shouldn't be manipulated manually or by non-Drupal processes (unless you're configuring an advanced workflow, really know what you're doing, and can accept the risk that Drupal could theoretically annihilate any "extra" files it finds as it has write perms).

If you're certain the folders you're talking about aren't managed by Drupal, and you don't need the contents, you can assume they're safe to delete.

Obviously you'll need to perform sanity checks to ensure other processes outside of Drupal don't rely on them first. Hopefully your infrastructure is documented (if not, now's the time to start)

FYI You can check whether individual files are managed by Drupal by interrogating the file_managed table.