Of course Disney can control scent in a theme park because for the most part they have control over that. Theme parks are predominantly artificial environments, not a natural environment.
WDW is reclaimed swamp land with a lot of water. Alligators live in that water, they can't be controlled. They are wild animals, and they can't be 100% controlled, it's just not possible. Five thousand warning signs probably wouldn't stop everyone from going near the water. Signs are like the security at theme prk gates: they are deterrents, they are not absolute guarantees to safety.
Of course they know alligators are there, and believe me they do a lot in corporation with state and local authorities to keep tabs on the wildlife population, and handle them as they become aware of individual animals.
This is not Disneys fault, this is not the family's fault. This was a horrible accident.