I think...you have done something of interest here...
I would make a few changes that you may see fit to observe or toss in the trash...
1) If you play God, then you should have only 4 units, Jesus Christ, Arch Angels, Saints and 'Devotees'. Christ would obviously be the ultimate unit, and Devotees would can only be built by the forces of God. Give them a middle range attack and low defense, but cost next to nothing.
2) If you play Satan, then you should have a greater variety of units: (but none as powerful as Christ) and you might try a couple specialized units- Satan (of course), Death, Pain, Agony, and Suffering. When any of these units are killed, they reappear in Hell to begin again but also destroy all evil units in supposed "sacred" lands. There should also be "free units" that appear at random called, "Imps". These guys have a low attack but a strong defense and they appear in "sacred areas" at random (they are the Spy Unit!).
3) Change the names of your Civs to:
Forces of Good
Forces of Evil
The People
Athiests
Scientists
Heathans
This way, it redirects some of the aspects from outright translation and gives more freedom to play from different points of view...Start the scenario so that "The People" are already allied with the Forces of Good, Heathans are allied with the forces of Evil, and Athiests are Allied with Scientists. The goal should be to capture and destroy "Hell's Fire" (could be a city). Obviously if you play the forces of evil the object would be to conquer everyone.
This is just a list of suggestions that might make the scenario better. Feel free to pick this apart and yell at me about what you don't like...but I thought I'd offer the advice.
John