It usually runs about 90 mins or so. What time is Wishes that night? If it's at 9 you may not get to MK in time depending on how long you have to wait for the boat. If it is at 10, you shouldn't have an issue getting to MK in time.
I would stay and see Wishes from the beach at Ft.Wilderness. They do pipe in the music and you do get to see it. Also, you may just have time to see the electric water pagent when it comes by.