In Day of the Moon, America is occupied by a hostile alien force contemptuous of humanity. The entire planet is occupied, and the human race is under a subjugation it doesn’t even know about. They’ve been there for thousands of years, it’s going to take something immense to get them to think that maybe they should sod off.
The Doctor doesn’t bring about a bloodless revolution, some of the Silence were killed by River (and why? because they attacked first), undoubtedly there were others killed by humans. But that is not genocide, and genocide is not what the Doctor wants. It’s clearly stated in the episode that what he wants is for the Silence to leave. “How fast can you run?” he asks. “Because today is the day the human race throws you off their planet.”
GUYS. He TOLD them to run. That’s all I’m going to say.