You gave me a scare there for a minute buddy, when you started to sound very re-assuring in the lead up to answering the guest who had the question about the alligators and Ameoba found in Florida waters, then of course you mentioned the number one reason why you are not going to be in danger from these things is of course the fact that Disney does not Permit swimming in the lakes (Whew!), you mentioned a bacteria rather than the Ameoba, and the thing I have always heard about IS an ameoba and it has caused deaths in central Florida here's an excerpt from an article on wikipedia
In 2007, the death of three children in or near Orange County, due to a rare, deadly infection,
Primary amoebic meningoencephalitis, also known as PAM, has prompted a public health investigation in conjunction with the
Centers for Disease Control.
[1] PAM is a water-borne infection caused by the amoebic organism,
"Naglearia Fowlerii", that enters the brain through the nose, usually resulting in death. PAM is associated with swimming and water sports in fresh water bodies and inadequately chlorinated swimming pools. An increase of
Naegleria Fowlerii may be seen with
global climate change, given that PAM is more likely in warm water.
[5] Orange County, FL has had 16 cases of
Primary amoebic meningoencephalitis, in 45 years, of 31 PAM cases recorded in the
State of Florida.
Anyhow like you stated, if you follow the rules you will be fine, the thing the folks on that other unnamed podcast were commenting on was the number of times they see people BREAKING those rules, often by playing in the shallow part at the waters edge, which unfortunately is where the amoeba is more likely to be, while I think that any WDW guest being exposed to that Amoeba is quite unlikely, Why take the chance?
As for alligators they do exist in the Seven Seas Lagoon, Bay Lake, and even in the Rivers of America in Frontierland as they are all linked, (I even have a photo of one in the Rivers of America, with what looks like a turkey leg in its mouth no less!), but I have heard, anecdotally, that Disney does try to keep an eye out for any larger ones that might need to be relocated, when WDW was first built alligators were an endangered species nowadays there probably aren't many bodies of water in Florida where there are not alligators, still the old adage of "they are probably are more afraid of you then you are of them" is most likely true (though I'm hoping that thing about trying to keep out the big ones is true too), as for the exposure to water guests might get while doing some of the water sports I'm betting folks usually board boats for these activities from docks at marinas, and consequently are not wading in shallow water where the amoeba are more likely to be found in the sand.