Unless I am playing a pure paragon or pure renegade, I leave the queen/breeder to die. Assuming over course that leaving her actually does result in her death. I don't blame her for the havoc her children are creating anymore than you can blame a human husk. I see her as an innocent victim, but one that poses to great a risk. It's obvious that the Reapers can just clone another queen to fuel the source of Rachni soldiers, but I see no reason to sacrifice loyal Krogan warriors to save her.
The risks I see her posing is not limited to the war with the Reapers. When I look back on the trilogy and think about all that we learn about the Rachni and the Rachni wars, I can't help but think that the "sour yellow note" that drove them to attack was not the work of the Reapers. I believe it was the Leviathan. The Reapers implant their ground forces with cybernetics, but there is no sign the Rachni in the Rachni war ever had cybernetics. The Leviathan use their thralls as they find them. Guide their evolution to better suit their needs. Considering what the Leviathan use their thralls for, the Rachni are a perfect fit. They can move to an area and multiply in a matter of weeks to service any need the Leviathan could have. Could be wrong of course, but it's how I see things going down during that war.
With that being said, letting the Rachni survive the Reaper war still leaves the chance the Leviathan will get their tentacles on them again and use them to take over the galaxy. Even if you take pity on her in ME1 and let her go, seeing what can happen in ME3... the risks are too great. Again, unless it's a pure Paragon run I kill the queen both times. I still fight myself on it everytime though. When faced with one of these questions, I ask myself "What is a Spectre's job?" The answer: To preserve galactic stability by whatever means necessary. Exterminating the Rachni does this. Letting an extinct species return goes against everything a Spectre is meant to do. It's a di*k move, but... put her down.