“No, they had orders from the top that were very much affected by top Presidential advisors.”
Feel free to name these advisors. And give us the evidence of these orders that were given to senior military officers. Otherwise you are just dealing in conspiracy nonsense that makes claims but never produces anything to back it up.
Anyone who believes that Douglas MacArthur quietly took orders knows little about that man’s life. He wouldn’t even take orders from Harry Truman which is why he was fired during the Korean War. And he wasn’t the slightest bit shy about saying exactly what he thought.
More evidence against your claim are the comments of Admiral William Leahy. Leahy was the most senior active American military officer in WWII, ahead of Marshall, MacArthur, King, Nimitz, Eisenhower, Halsey, the whole bunch. And he happened to think that using the atomic bomb on Japan was wrong, and said that the blockade and conventional bombing were enough to end the war. He makes no mention of others sharing his view, or of this view being suppressed by some unnamed advisors who you believe were in a position to overrule America’s senior military staff in the middle of a major war.