I always loved the design of the Queen but quite hated (and still hate) the concept of the Queen, so this "one-off" really jives with me. Even so, the Queen has become such a major aspect of the Alien universe, so by writing it off like that, great bodies of work would be written off as well, which in a way would be kind of shitty, to say the least. Only Ridley Scott could get away with something like that.
Other than that I do like Tristan's idea on how to wrap it all up.