We did the GF Pirate adventure this past Jan. I must admit I was nervous beforehand too, more because the children would be on the water without us than anything else. We had previously done the Disney childcare in the BC and on the Disney Wonder, so I had gotten over my fear of strangers taking care of them. Also, my children that attended were 8 & 6 (didn't let my 4 yr old go) and we've had many conversations with them about appropriate/inappropriate behavior.
That said, you are given a beeper when you check in. I made sure my kids knew I would be close enough to reach them and they could beep for any reason. As it turned out, the day they went in Jan was so cold (low 40's) the CM's didn't take them out on the pontoon boat but instead conducted the whole scavenger hunt in different parts of the GF and Poly. They even got the parking valets to dress up as pirates! I needn't have worried about the water thing - but if your 6 yo's are not swimmers (or comfortable in boats), I would rethink matters.
Disney does staff it very well. I can't remember the exact numbers - no more than 20 children - and there were 4 CM's assigned when I dropped off and picked up. The median age of the children there was probably 6 or 7.
My DD and DS loved it!!! Plenty of kid trinkets, candy and gum when they finally found their "treasure". They give them the Micket ears with the pirate bandana attached which is too cute! Now that the BC is offering the same activity, I'll probably do it again with my youngest!
Good luck with your decision.