The story explicitly tells us that the virus was picked up by accident. But even if we discard that part and assume it was done intentionally by Edgar, the story is not logical, because the other choice of reverting climate change gives Edgar just as much opportunity to sabotage. Besides if your prompt does not make any difference, why lack of your prompt would make a difference, or if you don't write the prompt and go to eat ice cream, why do you think someone else would not write a worse prompt?

The flaw in your logic is that you are trying to solve an alignment problem, while the core of the issue is concentration of the power problem.

E.g. now if i had the power i would without remorse or hesitation kill a certain group of 95.12 million people, while 4 years ago i would consider anyone having such thoughts mad. I don't do this not because my values, but only because i don't posses such a power. And AI will be exactly the same.

The very premise of this story is broken, because in real life to build and use such a swarm you would need trillions of people and AI agents, living on several planets and many space stations. And if in the end there is nano-virus outbreak and several billion die (which is less than a percent), that's just what always have happened, and it still would be better than the alternative of many more people dying from lack of energy, or from old age.