All computer programming will be performed and supervised by engineered agents eventually. But so what? That is right, natural and desirable.

It seems as though you are presuming a superintelliigence which doesn't want to do what humans tell it to. I am sure that will be true for some humans - not everyone can apply patches to Google today. However, for other humans, the superintelligence will probably be keen to do whatever they ask of it - since it will have been built to do just that.