Dan, I think you're overestimating the difficulty of the basic wiki family method.
Here is all that is required: * a single wildcard entry in Apache configuration * one or two lines in LocalSettings.php to pull a DB name from the hostname/path/CLI parameters.
As for cleaning up resources to keep the machine from getting clogged, it's very unlikely that your test wikis will fill up a multi-hundred-gigabyte drive in the middle of a run. If you find that they do, there's still no need to tie cleanup of any particular run to any particular other run.
All you need to know is which runs have completed and can now be cleaned up.
-- brion