Try something like this:
Code:
# Ensure the URL ends with a trailing slash
RewriteRule ^directory$ http://www.domain.com/directory/ [R=301,L]
# Rewrite the URL to grab the contents from the websites directory
RewriteRule ^directory/(.*)$ /websites/directory/$1 [L]
# Redirect /website directories
RewriteRule ^websites/(.*)$ http://www.domain.com/$1/ [R=301,L]
Not tested.
