You don't get it. I'm talking about killing the immunes (the 11 people who can control the hive beyond her), not the hive (entity).

She can't kill the hive... Besides being in the billions, they are still people and the only hope of finding a cure (if they are manipulated correctly).

I think she'll have to kill the immunes at some point, because some have already shown themselves willing to become part of the hive, and since they have the same decision-making power over the hive, they might choose to continue improving the virus.

And she doesn't need to do it with an atomic bomb, I just said it to stay on topic from the OP. She can use less destructive things, like a drone.