My take on this has always been (other than this being a simple plot hole caused by later screenwriters not really paying close enough attention to the first flick) is the "carnivorous gorilla" stage was either Cornelius misinterpreting his finds or else some sort of offshoot or survivor group that wasn't part of the society that became Ape City.
And of course, the apes always knew the truth about humanity, but kept it secret from everyone except a few high level types- Dr. Zaius being one of them.
As Zaius says, all his life he awaited Taylor's coming and dreaded it. He somehow knew the whole story from the beginning, including that humanity had once had a civilization superior to the apes'.
So, for me, all that "animal control" jazz is oppression because it's just a smokescreen to cover up the ape government's true purpose- preventing humans from reacquiring technology and destroying them, or some sort of misguided attempt to prevent Taylor from reinstituting human civilization. Or, alternately, pushing the Alpha/Omega button. Due to the alteration of the timeline in the later (chronologically earlier) films, we can't be too sure what exactly it is Zaius feared so much.
And also the apes' treatment of humans is punishment for having kept them as slaves. To the ape population in general, the humans are just animals. But to apes like Zaius, they are former rivals and enemies who could be that again.
Zaius is the ultimate hypocrite in some ways, but also a desperate creature with complex and somewhat conflicting motivations because of his foreknowledge of a terrible fate awaiting them all. And yet he still plays into Ursus' hands and helps precipitate the final disaster despite this knowledge.
In fact, if he had chilled out, apes might have lost their supremacy but the earth would've continued to spin through space for eons.
Too bad, Zaius! You screwed up, pal.
EDIT: About two minutes ago, I had another thought. Perhaps Zaius wasn't reacting to any Sacred Scrolls prophecies of Taylor's arrival, but rather to his own inference from his insider's knowledge of ape society's true origins that sooner or later, a human would appear with the power of speech, signaling the end of ape supremacy. Maybe that's the implication of his private argument with Taylor after Taylor's trial.
Either way, I think Zaius had multiple motivations, some positive and even noble in a certain light, and many others overly reactionary and paranoid. And in the end, the paranoia won out and he foolishly went to war with Ursus.
...............someday
