Why on earth would they take you out to the deepest spot first, especially if they know they will have inexperienced people on the boat? That is nuts? I knew there was a deep portion of the trip and was planning on skipping that part and staying on the boat but I had no idea it was the first stop!
Our second time on Jolly Pirates, I did just what you said - I stayed on the boat at the deep water stop, and I wasn't alone. The boat itself is fun, there's music and drinks and the staff is great. I would go again though if it was a day that was less choppy than our last time. I don't want to discourage you at all because Jolly Pirates is really a lot of fun. I just think the 1st stop is probably not the best. They staff does a good job at letting you know what to expect.
I have done the Jolly Pirates 4 times. The first time, I hated the first stop at the Antilla. Way too choppy and it was my first time snorkling. The pirates warned us, but I didn't listen. As they were helping me aboard, one of them said - we told you!! The second time, the waters were a lot less choppy, so I tried again and it was great. The last two times, too choppy so I stayed on board, had a run punch and watched the others. No matter which way you do it, you'll have fun. The Pirates are a great bunch of guys - they even let me drive the boat one time. We are planning on going again next year!