Damn, this was deep shit!
On one hand - I absolutely root for guys like Kidder. "Pure" engineers, scientists of any kind, academics are beautiful to behold. I imagine myself like that, if maybe I had had the balls to not succumb to the reality of Maslow's pyramid.
On the other hand - these guys who are too committed to their fields might be rather too psychotic to be good for the good of the world - that is, even if we don't get judgmental about the moral weight of their actions. I personally do not know anyone with such a mad, evil, scientist bent of mind. But hey, the fact that society came up with, and deployed the N-bombs shows we are capable enough. And Elon Musk, huge fan btw, might be going down that path.
And then, there's the theological aspect of the story. As much as I want there to be a benevolent God, I am afraid I am atheistic in my outlook. But sometimes I do think that if God exists - it might just be an entity like Kidder. Not necessarily evil. But just has its own agenda, and while it doesn't want us to go extinct, it wouldn't mind killing off a few of us if it somehow helped create what it wants. The Kidder-neoteric relationship was a perfect depiction of our species' relationship with God, all things considered.
Now those are deep waters to tread in - and as a short story, Microcosmic God is very, very successful in handling that.