I've pushed mk-project version 1.2.1 to both the Emacs Wiki and github. It fixes a bug that was preventing mk-project from killing dired buffers open to a project's basedir (or a subdirectory of the basedir) when the project was closed (and the user elects to close all project files). You can now also expect dired buffers belonging to the project to be restored when the project is re-opened.
Thanks much to email@example.com for the bug report and code.
For more info on mk-project, see its homepage.