I don't want to start anything about casting Japanese people in a bad way, but at the time, in WW2, I doubt there would have been anyone on Okinawa that would have given blasting six Japs that might have been surrendering a single thought, much less a second thought. Almost all Japanese soldiers were killed or commited suicide. Japanese were programed to believe that surrendering was worse than death and they really took it out on the Allied POWs. Also, you don't need a rifle to kill (grenades, knives, strangling), anyone leaning over the CO at night, I don't care how many "white flags" they had, is looking to be shot. I think if Thompson didn't get rid of the flag, his CO would have. I don't think anyone would have cared in that situation. And I think Thompson is the only one who does, and that's the point. He didn't say "they had a white flag and I killed them anyway" he said, "after I killed them I saw they had a white flag" That makes a huge difference. But YMMV and so on.
Real world story: My dad was on Saipian, Ie Shima and Okinawa with the 318th Fighter Group. One day he saw a Jap soldier walking toward him with his hands clasped behind his head in a surrender gesture. Well, unfortunately, it had been a standard trick for Jap soldiers to hide a pistol or a grenade behind their heads while pretending to surrender. Dad kept motioning "hands up" with his rifle, but "that Jap kept coming and jabbering at me. So I shot him." In the face. With a Garand. The guy's hands were empty. Dad said he felt bad about that, but they kind of brought it on themselves because of that grenade trick. Dad suffered no disciplinary repercussions.