I think that some brides have done this.
Cost varies depending on the desserts you choose, plus guests either have to have a ticket to EPCOT, or you pay a viewing fee per guest (I seem to remember it being $12.50 per guest, but I may be wrong.
Anyway, I think it's a great idea, except...time frame. You would likely have quite a few hours in between your wedding and the dessert party, what would your guests do? Since it would be an intimate, you won't have many people to worry about, but it's something to consider. If you had a late afternoon ceremony, you could do a wedding dinner and then head off to the dessert party...I think that would work. The last time I checked, the latest you could have an intimate was like 5:30pm.
Don't forget, as well, there are fireworks cruises available. Private dining can even have things like chocolate covered strawberries and champagne served on board. I think the pontoon boats will comfortably seat at least twelve...but I may be wrong.
Happy planning!