First of all, OP, I am sorry your son was injured. That is no fun no matter how it happens.
Second, I have to say I am really shocked he went back in the water with open wounds. Aside from being concerned about bacteria from the water getting into the wounds I would think the chlorine in the water would sting the snot out of him. Maybe not though.
Just as an aside, if you are aware how powerful waves can be as you say you are, I guess I'm confused as to why you are so surprised how powerful the 6 foot wave in the pool is. Waves can be really powerful. I assume you mean you have experience with waves in the ocean. While true, there may have been sand under your feet but I'm sure you have experienced an undertow from time to time.
Also, you had to have known exactly how rough the bottom of the pool is when you first stepped into it. Is it a bummer that the bottom is so rough? Yes. Is it necessary? Yes. Sure would be nice if Disney could figure out a way to make the bottom provide traction but not be so rough. Maybe some day.
I remember when I was a kid that after the water got to be about 4 feet deep or so the bottom was completely smooth. And let me tell you, it doesn't matter how strong you are when that 6 foot wave hit you on the smooth bottom you were getting knocked over. I can see how that would be REALLY dangerous.
Did you not watch the action of the waves a bit before you went in? Maybe it's just me but I always check a ride or slide out, as much as I can anyway, before deciding to go on it.