nixos/lib/test-driver: clean up threads correctly

The current implementation just forks off a thread to read
QEMU's stdout and lets it exist forever. This, however,
makes the interpreter shutdown racy, as the thread could
still be running and writing out buffered stdout when the
main thread exits (and since it's using the low level API,
the worker thread does not get cleaned up by the atexit hooks
installed by `threading`, either). So, instead of doing that,
let's create a real `threading.Thread` object, and also
explicitly `join` it along with the other stuff when cleaning up.

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