I'd turn the truck off and leave it in gear.. There is no way the weight of the trailer is going to pull it in the water, especially with the e-brake engaged... Make sure the boat is unhooked before it even gets close to the water (tiedowns, winch, etc)... Even if you somehow screw up and the truck goes back a few feet, the boat won't be attached to the trailer so it won't pull the rear wheels of the truck off the ground..
If I was using a 2wd truck, I'd always have a winch just in case.... Nothing worse then 2wd and no weight in the bed... Pretty useless.