A nice concept, and to add on that, I think that Dragon Age II's overall take on such issues would be a good place to start- the game shouldn't have a set ideology that it's preaching (i.e. spirituality=good, religion=bad), but it will be up to the player to find his/her way through morally grey areas to eventually take a stand that s/he agrees with. DA2 did an overall good job of not portraying either side of the main conflict as the overt bad guys, even though the plot continuum near the end absolutely fell apart. One way not to do it would be like in Baldur's Gate II, such as when the player is faced with the choice between Bodhi and the Shadow Thieves, the game made it pretty clear on who the villain was.