I'd talk to some of the other parents before raising a big stink, but definitely talk to the teacher about your concerns. Honestly, it sounds like a fun field trip to me, though I can see how a sensitive kid wouldn't have a great time. I'd actually prefer this greatly over the usual candle making thing. I dislike the emphasis on "quaint handcrafts of ye olden days" that a lot of living history museums and most school projects concentrate on. It makes the past seem very quaint and wholesome and fun, when it was actually extremely dirty, hard, and dangerous. I think it also teaches kids that handwork and simple things like baking belong in the olden days, and helps reinforce our cultural norm where we lack respect for production and doing things by hand. Don't get me wrong: I love visiting living history museums, but they do present an extremely idealized view of what life was like for practically everyone.
I'm assuming they served other things for the kids to eat than onions, right? Was it an onion-based meal, or were the kids just encouraged to try a small piece? And I've never been on a boat where there wasn't a lot of yelling. When you're sailing, things have to be done quickly and there really can't be much room for goofing off. I can see how he'd find it unfair if he got yelled at for other kids fooling around, but maybe they thought that he was fooling around too, if the rest of his group was. If he was supposed to be in charge of these other boys, the teacher should have stepped in at that grouping if she thought that their personalities conflicted and your DS couldn't get them to behave. Sometimes that sort of thing works, and sometimes it doesn't.
I think the success of this sort of thing really depends on the child's temperament, and it's unfortunate that they didn't give you a heads up about what was this trip was going to entail. The school should have been more clear, so that you could have kept him at home.
As for the lack of female chaperones, I assume it had to do with sleeping quarters. For example, if the boys slept on deck and the girls slept in the cabins, then there could be only room for the female teacher down below while plenty of room for extra men to sleep on the deck.