"Scientists were concerned"? Scientists were in charge since the Generals didn't have a clue. The problem was that the Truman administration wasn't concerned.
Scientists may have been making the day to day experimental decisions as the Trinity test approached, but it was still an Army project. I doubt the Truman administration knew enough to be concerned or not. By the Trinity test, Truman had been president only a few months and he had many other things on his mind. As you said, the Army didn't have a clue. It was all too new.