I think there is little if any chance the argument will prevent the prosecution from moving forward in THIS case. But, like I said, it's an interesting legal question. I am reminded of the movie "300" where the Spartans simply dispatched the negotiators without further adue. How rude was that!
How does America typically deal with negotiators during time of war? In THIS case an argument could be made that the pirate came aboard seeking medical aid for his injured hand or simply wanted to give himself up. It is not clear cut that he was under a flag of truce, or so I gather from the news reports.