That is the general idea; just with a script that gets called any time the cert is renewed (--deploy-hook).
But I'm not certain where you are actually using the cert...
From your post, only these lines look related but they are rem'd out:
/etc/lighttpd/lighttpd.conf:# server.name = "vorman.mooo.com"
/etc/lighttpd/lighttpd.conf:# server.document-root = "/var/wwww/html/owncloud"
/etc/lighttpd/lighttpd.conf:# ssl.pemfile = "/etc/lighttpd/certs/lighttpd.pem"
So...
Can you also show?: