I don't think there's any reason to believe that the zoo has significantly changed since Steven was there. The humans inside were happy and healthy, but raised to be completely dependent on their habitat and caretakers. Even if they were moved to Beach City with people who knew their situation, they'd probably still be unable to care for themselves or handle reality in any capacity. The show made it clear that they're utterly incapable of even dealing with minor sources of emotional stress, much less the real world problems that humans typically experience.
Unless Rebecca Sugar or someone else on the team clarifies differently, I think it's safe to say that the zoo is still there with the humans living in it. Abolishing it, in my opinion, would be unethical. Steven may have convinced Blue Diamond to simply stop letting them breed so that new generations aren't born and the current population eventually dies out, but that's just speculation.