I have never purchased rice crispy treats at Walt Disney World, so I don't know whether they are any different from those on the cruise. My guess as to the reason for the cost difference is that the treats at the parks must be packaged for sale and delivered to each location where they are sold, while those on the cruise are stored en masse and don't require as much packaging and transportation. That is strictly a guess, though.
On our last cruise, I stopped by Guest Services near the end of the cruise with a quick question and was offered a bag of several Mickey treats. I wondered if perhaps the treats were nearing the end of their shelf life and GS had been told to hand them out so they wouldn't go to waste. If there is a shorter shelf life, that could also account for the price difference.