General Milley, his friends say, has agonized over the events of the past week. But he has also managed to persuade Mr. Trump not to invoke the 1807 Insurrection Act to deploy active-duty troops across the country to quell protests, a line that a number of American military officials say they will not cross, even if the president orders it.

It is largely because of General Milley, administration officials say, that Mr. Trump has not ordered it yet despite his threat to do so.

The general went face to face with his boss on Monday during a heated discussion in the Oval Office over whether to send troops into the streets, according to people in the room. He argued that the scattered fires and looting in some places were dwarfed by peaceful protests, and should be handled by the states, which command local law enforcement and the National Guard…

Once Mr. Trump arrived at St. John’s Church, holding a Bible, and it became clear that the moment was only a photo op, General Milley disappeared from view. He is nowhere to be seen when the president motions for other officials to join him for a photograph, in which he is now flanked by his press secretary, defense secretary, national security adviser and attorney general.