You have to take the game a bit too seriously and immerse yourself in the role to justify killing her rather than releasing her.
If the history of MEU was real then, given what you know at the time, There is no guaranty that the Queen is being straight with you and not just feeding you a line of BS to save herself. She might be telling the truth or she might be planning galactic conquest. You know nothing about her and ridiculously little about the rachni in general,. This 'sour yellow note" is just cryptic nonsense that could mean anything. What you do know is that ever free Rachni you have met has tried to kill you. The entire history of the Rachni is them trying to kill everyone. They can control the dying and breed at inconceivable rates.
Suppose that after hearing the Rachni Queens story for the first time and you believe every word. That their entire race fell prey to "voices of oily shadow" that forced them to go to war with the rest of the galaxy. A war that lead to the near extinction of every space fairing race. That, if not for the Krogan, there would be no Asari, no Salarians, no Quarians, no Turians, no Elcor, no Hanar, no Volus, no Batarians, no Drell all because the Rachni heard a "sour yellow note". Is there any assurance that this note isn't still out there? Can you be certain the "voices of oily shadow" will not force this queen and her children to wage war on the galaxy once again?
IMO, the risks are simply too great and the unknowns too sweeping to release her. It's too dangerous. Besides, the purpose of the Spectre's is to maintain galactic stability not destabilize it.... you still feel like a total d^ck afterwards though.