Yes, but the people making those threats aren't the people who were killed. As you yourself say, they were civilians; and they certainly weren't in Manilla.
So were those in Tokyo and the other 72 cities levelled in bombing campaigns on Japanese homeland prior to the two additional cities of Hiroshima and Nagasaki.
But i'm not sure what your point is. If you're referring to the tragedy of those civilians killed in Hiroshima and Nagasaki, it's grotesque, but how is it different from the tragedy of million of civilians killed by the Empire during its conquests, or the hundreds of thousands of civilians killed by the U.S. bombing raids with conventional weapons before the nuclear bombs were dropped, or most crucially, the possibly millions of civilians and soldiers who could have been killed if the American forces had directly invaded?
Under the lack of foresight at the time, and given the nature of Japanese belligerence, it's not hard to understand why the U.S decided to drop the two atom bombs, given what they'd already done while still facing Japanese intransigence. Maybe it wasn't the most moral of choices, but under the circumstances, it had an understandable logic of hardened pragmatism that it's too easy to sweep under a rug of condemnation today with foresight, which itself might be mistaken even now.
