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One can debate whether they should have or not... but they clearly thought this was something that a) took special consideration, b) was not merely a military decision, c) had unusual (for a military operation) civilian oversight, and d) presented new moral and policy questions.
And — in fact — they thought it was VERY IMPORTANT to convince the Japanese it was something different, too. Because they wanted it to have an effect. The people who argued it was no big deal were the people who thought they were getting overlooked as a result — e.g., the USAAF.
