If you read carefully, I think you are a bit off base here. This situation is unique in that the player cannot be substituted until after he attempts both free throws, but because he missed the second one, there is no stoppage of play for him to be subbed out. Once he misses the second (and there is no foul on the rebound or instant timeout called after the rebound, etc.) the game should go on without a stoppage, therefore the substitution here is logistically impossible.