I don't personally subscribe to all the lake madness.
Yes, there are gators (It's Florida!), but then again most ocean beaches have sharks, so being vigilante is all you can do unless you intend to only swim in chlorinated water. As for the amoebas, again vigilance. Know the risks and how to prevent infection (wear noseplugs, etc.). The problem I have is that if Disney says stay out of the lakes...STAY OUT! You are on their private property and they have the right to make their own rules! Whether or not you are scared of gators and amoebas (I'm not for the reasons I have given) is irrelevant. Rules are rules for a reason. Don't think for a second if it was feasable to open the beaches Disney would keep them closed. Wow, I think I sort of channeled Pete for a second, LOL!