The amoeba lives in the sediment at the bottom of the lake. That's why swimming was discontinued in the lakes, because doing so would stir up the bottom where the amoebas lvie. Skiing, boating and other water sport take place out in the middle of the lake, where the water is deep enough that people won't come anywhere near the lake-bottom.
I agree that things could have been altered, though it wasn't as simple as warming and chlorinating the water. From what I've read about how RC operated, the entire system would have had to be altered. Most of RC's water systems (except the traditional heated swimming pool) created a constant loop of lake water. Water was pumped into the park for the slides, it flowed from the slides into the main area of RC, and then out over the inflatable "bladder" near the water that formed the barrier between the lake and the park, and always kept the water level in the park slightly higher than the lake.
So the entire system would have to be re-built to permanently separate the park from the lake, and then re-plumbed to take water from the swimmin hole and put it back into the slides.
As you speculated, Disney was unwilling to go to those costs, especially when they had other more modern water parks on-property.
-Rob
