I let it live.
It was a sentient being, able to express thought and display consciousness. It was innocent of any crimes of its ancestors, so killing it just because of its species would have been a gross violation of basic rights.
Plus, a Rachni swarm with a favor to return would be a kick-ass ally, and I'm surprised Bioware never explored that in the story.
Mass Effect presented some interesting moral choices. Still doesn't approach much real world morality, but some of the decisions you make seem to have more weight than in similar games.