Let me ease your fears. My six year old granddaughter did this at the Grand Floridian. It was her Christmas present. I had her mother's approval. But when we all got there, I don't think my daughter-in-law realized that for the next two hours, her baby girl was going to be out of her sight with 23 other kids she has never met. Her fears were quickly erased.
You will check in your child and be given a receipt and a beeper. You will need BOTH to get your child back. You will help your child pick out a life vest. A Cast Member will check the fit of the lift vest before your child boards the pirate ship. About five minutes before the start of the cruise (make sure you are there fifteen-30 minutes early), the kids will be gathered together and given their instructions. Since your son is going solo, he will be paired up with another child of the same age range. They are told they are buddies and to do everything together. At exactly at the start of the cruise, the children will be marched two by two on the pirate ship (a pontoon boat with a Jolly Roger flag on the back). You can clearly see all this going on. The kids will give the adults on shore and big wave and they are off.
Get back to the dock a little before two hours later and you will be greeted by a whole boatload of very happy children. And I mean greeted. If you have a video camera, make sure it's on. The Cast Member will take each adult's receipt and beeper and then the appropriate child(ren) will be let off the ship. They get lunch (uncrustable, juice, and something else). My granddaughter didn't eat it at all because she was too excited.
When you check you child in, you will be asked of any allergies and they will accommodate the lunch if needed.
My daughter-in-law was actually not nervous at all after seeing how Disney did the whole thing.