The use of "wisdom" in the context of sapience isn't sagacity, in the sense of "wise old man passing down knowledge and teachings", but instead the ability for insight, introspection, active judgement, forethought, and comprehension, IE the indicators for intelligence beyond the instinctual, things which are important for human-level intelligence. When people say "sentience" to mean "some thinking and reasoning being of at least equitable level to humans", the actual word for that is sapience.

I myself can not see Zodiark creating said ameobas and allowing for evolution to take place again naturally.
I don't know about his initial recreation being microscopic life exactly, but we are told directly that their plan was to allow life to propagate naturally on it's own until their was more than enough for them to sacrifice part of it to restore their people. The point I'm making is that we're never given any indication that this life that was meant to propagate was that of the intelligent or human-like variety. If we want to speak in terms of logistics here, the sort of life that would spread the fastest and not take too much from the environment would probably not be humanoid, but instead various kinds of plantlife.
I will say that Zodiark probably did need to create microscopic forms of life in addition to whatever else though, because from what we're told of the nature of the calamity every living thing was dying.