I'm sure that the gator excuse is valid but I think the real reason is the water is polluted/contaminated and you don't want to be turning off the guests by saying this. Remember, Seven Seas lagoon was man made when they built WDW in late 60's and early 70's and is not a natural lake. Think about all of the pollution from the boats, Water run off, Acid rain, and people since WDW opened in 1971. If you take a look at the first pictures of the Polynesian in the early 70's you can see people used a roped off section of the lake for swiming (Check out Tikimans website) but times have changed. It's impossible to keep a lake free of bacteria like you can a pool and that's one of the reasons I don't swim in lakes anymore.
Plus add in the Gators and the poisonous snakes and you wont dare to go into that lagoon. There is currently 6 types of poisonous snakes found in Florida, 2 of which live in or around water. Stay alert! Google it if you don't believe me I'm kind of a snake buff and I'm facinated by them, yet afraid of the dangerous ones. I'm not trying to scare anyone just make them aware. Remember, forewarned is forearmed as a wiseman once said!
There is no reason to swim in that dirty water when WDW has some of the best heated and cleanest pools around. Lakes are hard to clean, pools aren't!