I'm a big coaster fan, but water drop rides still manage to freak me out. If your son likes coasters, then I'm sure it's probably not the fall on JP that scares him as much as the fear of the fall.
I think the distiniction between coasters and water drop rides is that, with coasters, you feel anxious for a few seconds as the train climbs the hill, but get to experience exhiliration for the rest of the ride, yet, with water rides, you're anxious and nervous for the entire duration of the ride to the top of the hill, and then feel the thrill only at the end, for a few seconds, as you drop.
Your son has two options. He can either choose to be scared of the JP drop, and simply skip the ride entirly, or he can decided to over come his fear by arriving early to the park, when the ride wait is zero, and riding it five (or more) times in a row. Much like a rollercoaster, after doing it a few times over, you get used to the drop (and the anticipation), and don't have a reason to scared anymore.
Since he probably likes coasters as much as I do, I'm sure he's more bothered by the fact that he is scared of the drop then of the drop it self, so I hope he takes the second option.
-Kevin