I'm not sure why Disney doesn't allow swimming in their lakes - but I'd bet it has to do with safety and lawsuits!!!
I swam in Seven seas Lagoon (along with 1000 other women) in Sept. '02 as part of the Danskin Triathalon -----Danskin runs this triathalon at WDW every year (It was last weekend I believe).
There are no warnings or other advisories given regarding the water---and seeing as this is a "baby triathalon" for athletes of every ability -- there are quite a few women who are not the best of swimmers (there are "angels" in the water with noodles for those women to rest during their swim!)-- hence, there is probably alot of water-gulping.
I saw one fish swim into my legs, had seaweed stuck in my bathing suit, and certainly gulped my share of water (it's almost impossible not to, with that many people all trying to swim at the same time in the same place) -- But nope - I didn't get sick---In fact, I've never heard of anyone getting sick.
It may be true that they treat the lagoon prior to running the triathalons, But knowing Disney - I bet it's safe all of the time (see aforementioned lawsuits)---Maybe it has to do with erosion of the lake, wildlife in the lake (I'm talking fish here) -- who knows---but I doubt it's amoebas.