Except that it's a pirate ship. It is in port flying no flag and not being hostile. Outsiders have no right to come into a city and start destroying ships in port. It's illegal. Osama has no bearing on a boat in port.
Your example falls down when you compare it to two enemy civilisations. If two civs are at war and you are at peace with both, then it would annoy your government supremely if one came burning down ships of the other while they were resting in your port. Although this is technically possible in civ it is still a flaw.
Also, even if you somehow accept that random troops can enter another civilisations' ports and start burning ships down, there is the issue of one having JUST completed a pirate ship, only to have it destroyed before you can use it. How do they know it's a pirate ship? It has never left port, has no reputation, and the flag it flies is irrelevant. Again, very obviously a gross act of vandalism!
Al