I am assuming you are asking within the Share sites?
I'd try this, go into the Alfresco Repository Application, Alfresco Explorer, and remove the read EVERYONE permissions from Company Home, see what happens in Share. Remember though, that since all subspaces in Alfresco Explroer by default inherit, you may possibly need to whitelist the permissions for people to see certain folders in Share (though, I believe it's taken care of by group membership).
Then, in Share, you'd have to modify the javscript, or freemarker template to evaluate who the current user is to display the repository link or not.