YOu have not been found guilty of anything. If he continues to harass you, have your attorney write a letter to his boss professionally stating your concerns. I would not put the mufflers on until I was found guilty of something. On the other hand, it might be nice just to "buy some time" by putting on mufflers. That's a personal choice.
I think it is a total crock and it is borderline harrassment. They have a job to do, but it seems this guy had a hard on for you way before he stopped you. Is he new?
Good luck, this is only the beginning of this garbage. I agree...all in all, we typically take better care of the waterways than the avg recreational boaters....BY FAR!!!!