While I agree with your assessment of the Rachni queen dilemma - I saved her every time -, it would feel wrong to me if there was a "right" decision.
I feel you lack the necessary knowledge about the nature of the Rachni, their history, the queen herself, etc. to make an informed decision. Of course, the game forces you to make a black or white choice for dramatic reasons, but I sorely missed the sensible third option (postpone the decision, keep the queen in custody).
I chose the right option to let her go. As an individual she did nothing wrong. But the third option of custody would make sense. But would that be fair? I'm not sure it would. Actually I'm pretty sure it wouldn't. Her captivity would have meant more experiments.