I don't think you want to change the permissions on the Primary web site. What does that accomplish? The default settings allow you to host a web site.
As far as deleting the Primary I-Bay, I suppose you could, buy why? If you want nothing in it then reduce the permissions to chmod 700. That way if there is a problem in the future you can change the permissions back to the default (755) setting and no harm done. If you are really paranoid then chmod 400 the primary e-bay. This will prevent anyone from writing or executing (including you) in thar I-Bay and allow you as root to see that I-Bay only. Therefore that I-Bay will never be larger than a few directories and one index.html file that no one can see. Then if it causes problems in the future, then "chmod 755 primary" and everything is back to normal.