Maybe it was in their plans. However they had hundreds of years to play with in the original timeline...

Free labor is nothing to sneeze at and the alleged revolt was, in their mind, generations down the line. Someone else's problem....

At the end of the 3rd movie, the only people who knew the prophecy were the President and the select committee. Since they thought they had killed the only super-intelligent apes, the threat was over. There wouldn’t have been any reason to incite panic by spreading the rumor or acting on it, so the whole affair was probably hushed up. The #1 rule of governing is NOT to tell your citizens that the sky is falling.

In this movie there’s a scene where they’re interrogating Armando, and they ask him if he’d ever seen or heard about Cornelius. He says no. Later when they hook him up to the truth machine he says yes, which signals that he was a conspirator. This backs up the idea that Cornelius, Zira & Milo/Caesar were kept secret from the general public and only an insider would know they existed.

(Mild loophole since Cornelius & Zera were celebrities in the 3rd movie, but maybe we can assume after 20 years no one would be expected to remember them)

The higher-ups at Ape Control were aware of the prophecy but lulled into a sense of security by thinking all the super-intelligent apes were dead… everyone believed this except the psycho Governor who hated apes and did everything in his power to exterminate them. But the general public wanted apes (free labor) so that probably stopped the Governor from outright genocide.