Here is an excerpt from the RCCL Cruise Ticket Contract:
Passengers are solely responsible to maintain in their possession all passports, visas and other travel documents required for embarkation, travel and disembarkation at all ports of call. Passengers assume full responsibility to determine through their travel agent or the appropriate government authority the necessary documents. Passenger agrees to provide to Carrier (at Carrier’s reasonable request) any travel documents. Carrier shall return such travel documents to Passenger by no later than the end of the Cruise.
Seems to me you are on very thin ice. The booking agent isn't really a seasoned travel agent and, in any event, making sure you have all the correct travel documents is your responsibility and with the unusual birth certificate situation you seem to be aware you have well...
You're probably correct that the agent at the 'exception desk' had a busy and stressful day.
Good luck pursuing this one.