After reading that article, I am convinced that Kerry was frightened, and that is why he used the little known clause to leave Vietnam early, and why he had those "injuries" that allowed him to do it. There is no doubt that the duty was dangerous, and that's why I think he ran.
That aside, he took his boat out of harms' way when the other boat was hit by a mine. He abandoned his comrades. The other boats remained at the site and rescued the men who were blown overboard. He only returned when it was safe and that's when he picked up Rassmann, the phony.