Actually, it doesn't destroy the idea of there being a Queen. The Aliens are much like bees, in that when they are without a queen one of the soliders will metamorph into a Queen. I'm not sure of the specifics behind it but it has to do with pheromones.
If you want check out this site: The AnchorPoint Essays
http://www.geocities.com/Area51/Corridor/3119/
There is some really impressive information on everything about the Alien.