God isn't even an evil figure, I know people always want him to be but its stupid. You talk to Metako, Suika, and Lilith; the magical girl system did at one point have a point for existing, it was actually a good or important thing early on. Demons often went wild and took control, they had to be sealed away. Even sealing them away rather than killing them is seem as some sort of mercy. And the angels, even if a bit stiff in their ways are presented mostly as alright guys in this series.
However god never accounted for a time when the system would no longer be necessary. So he never thought to turn it off. He just left it on as a failsafe, but didn't realize demon blood would dilute to such a level that they're basically humans at this point.
The moral of this story is always the help and save everyone, not to usurp god. Shamiko's ultimate goal is just to turn off the machine god left behind, to put a stop to the magical girl system, not to fight god. If god knew demons would no longer be a threat I'm sure he'd understand.