By this time, we all instinctively know the answer to this question. Lt. Decatur, upon his return, would be arrested and brought before a courts martial. Given the pitiful attitude of our government and its liberal adherents, he would be found guilty and jailed for the remainder of his days.
It appears to me that some practical things could be done to deny access to our ships by pirates. I wonder if their access path involves a ladder and, if so, could such be made retractable. That retrofit might cost a few thousand but would be well worth it. Barring that, a security force randomly placed on ships might be advisable. By random, I mean that every other or every third ship would have a security force placed in a random manner so that pirates would not know which ship was armed.
For more facts, and less criticism of Jefferson:
http://www.jcs-group.com/military/navy_marine/1801tripoli.html
The movie opens along the coast of Brazil -- an intial fight leaves Aubrey's ship damaged and gives the faster French ship a good head start. Aubrey pursues and get down to the Cape of Good Hope (if I have that right) and runs into fierce storm. An aide tells him, "Their ship is bigger, faster, and we will never find her in the Pacific. And now this storm is tearing our ship apart! Perhaps we are exceeding our orders in running such a great risk."
The captain looks at the man and says, "My orders were to pursue him as far as Brazil. I exceeded my orders a long time ago."
And of course, in the end, Aubrey captures the French ship.
I know it's fiction, but once upon a time, military leaders were expected to use their judgment.