OP, I think you made 2 mistakes. You should have brought it up during the cruise like where are the soda? Or "Are you guys really charging for coffee when lunch is supposed to be provided?" They can't do anything about the weather, but something they could fix. Now when you come back to dispute the charge, you didn't ask to dispute the entire charge. Instead, you asked for a 25% refund. That's like kryptonite to your dispute. Think about it... so you are okay with the service but you don't think it is worth the entire charge but a 25% discount will make you happy. What is the supervisor handling the dispute going to think? Oh this guy just wanted a discount. Next time he is going to a restaurant and not liking the food going to ask for another discount....
If the tour was so horrible that you and your family found it less enjoyable than not going, than you should just try to dispute the entire charge. You could tell the supervisor that once departed, you guys were stuck on the nightmare tour. But if you really think it is only 25% overcharge, than just write a honest bad review and let the next person know and move on. The tour operator may even fix what was wrong or offer you a partial refund or future credit.