The football throwing has screwed up the natural pronation due to the effects of how the football is thrown using mainly the middle finger and the thumb. This gives the hand a tendency to roll off the ball, but it also causes the elbow to hyperextend when throwing a baseball using those same mechanics. This is due to the fact that when throwing a football the hand has a tendency to end-up facing open instead of been closed.
To eliminate this problem run your son through this drill. Paint a ball black on one side so that the ball ends up half black and half white (let dry). Place the ball in his hand using a two seam finger grip. From a similated pitcher's set position have him throw the ball so that the black and white come out of his hand with out tumbling, eg., the black side doesn't change in flight. Make sure he points his index finger, and that the palm of his hand and his fingers finish in a goose-neck configuration eg., pointed down toward the ground. This will insure the elbow is naturally pronated.
After my son played QB during the football season he had the same problem. It would take several weeks for him to get his baseball throwing mechanics correct.