Empirically, we're killing the apes. (And by the way, that seems like a much better source of concern when it comes to alien judgment. Though the time for concern may have passed with the visible Neanderthals.) If Dr. Zaius goes back and tells them they could create a different "human race" with the desire to not do that, only a fool of an ape would refuse. And I don't believe in any decision theory that says otherwise.

I agree.

The question is: are there different constraints that would, either as a side effect, or as a primary objective, achieve the end of avoiding humanity wiping out the apes

And, if so, are there other considerations we should be taking into account when picking which constraint to use?