You can just not have anything link to the directory handler object in the database and not assign it an extension - then no callers can get to it and its effectively disabled.
You can also set its scope to, say, a COS that contains no users - although this is not very friendly since it'll allow users to try and find a subscriber by name and just never find a match.
You can also use Bulk Edit to set the "list in directory" option for all subscribers to false - this again just means no outside caller will find any users via any name lookup handlers.
