I too have heard about bacteria closing RC and the reason for no swimming in Bay Lake. I have to dispute this through mere logic however. The simple fact is that there is swimming allowed in Bay Lake. During Iron Man and similar competitions for example. Also when you do Sammy's Parasailing you get wet with lake water. If it was so dangerous would they risk people swimming in these events?
This is because they are swimming in deep water at the surface and are relatively safe. The protozoa live in the sediment at the bottom and when it gets unsettled (such as in shallow water by human feet) is when they become active. When people go underwater and don't plug their nose when the sediment has been unsettled, this allows a pathway for the protozoa to enter the body via the nose. Unfortunately, RC met about 3/4 of this criteria as the lake-water section had a natural sandy bottom.