Yes, running 'make deinstall clean' or even 'make deinstall distclean' (that wipes the tarball as well) in the port directory is the way to go. Another option is pkg_delete -f (or pkg_deinstall, which is a wrapper around pkg_delete), but that will only wipe the installed files, it will not clean the port directory nor will it remove the tarball. For people running pkg_delete/pkg_deinstall only, it usually pays to run portsclean -CDD(L) once in a while.
I usually delete only the obsoleted distfiles with portsclean, as it can happen that I want to install it again but (internet is broken)|(distfile in not available anymore)|(the only populated mirror has 1kbps down rate) etc.
So I can safely use pkg_delete, e.g.
If you make a habit of installing ports with 'make install clean' or 'portinstall', pkg_delete will be enough, because you will not need the 'clean' part of 'make deinstall clean'. The earlier remarks about cleaning out outdated tarballs with portsclean still stands though. In my opinion, using 'make deinstall distclean' saves work in the long run.