My girls are very small so I haven't had to face this as a parent. I do know that when I was 9 and my cousin was 12 he and I were allowed to do things on our own, but we had to stay together. We were both responsible enough to understand that meant if we disagreed we had to find a resolution ourselves. WDW was much smaller then, but we went swimming, to the resort beaches and rented boats while our parents explored the parks. No such thing as cell phones then! We did great, and had a ball. If your boys are responsible enough to follow the rules, then I think WDW is a good place to allow them some freedom. It is not a perfect world, but inside Disney Quest there is plenty of staff so if they need help it is close by. If they haven't been allowed to explore off by themselves on a trip yet, maybe start with letting them go to the resort or into a close by park on their own, and let them show you they can be where they are supposed to be, when they are supposed to be there. They have a phone they can use if there is an unusual delay like bus trouble to let you know.
That was always our number 1 rule - be where you are supposed to be, when you are supposed to be there. And if for ANY reason you won't be, you have to call. It has served me well, and will be the rule my children learn first too.