Fantastic article and subject matter!
"It [A morality system] might quietly take account of the player's actions without actually confronting them."
This part reminded me of Chrono Trigger. In the beginning of the game, you go to this fair and talk to NPCs and do other fun things that seemingly have no consequence whatsoever. Hours later, you find yourself on trial where the outcome is partly influenced by some of the actions you did at the fair: Did you help the girl find her cat, etc? Although religion isn't a key theme in Chrono Trigger, I feel that it masterfully handled morality by delaying the outcome of one's actions. As you can imagine, it encouraged one to go back and try different things to see their impact.
Lots of good quotes in that Robert Ingersoll article!
Regarding your game, maybe have a system where the player doesn't initially fit into any of those regional religions. But as they play, their actions align them towards Islam, Christianity, Zoroastrianism, etc. What may be a "good" decision for one religion may be a "bad" decision in another.
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