The possibility of more religious gaming is in some ways worrying.
I think that if people treat games as a vehicle for preaching there will be a bias towards one religion, Christianity. It dominates the countries which own most of the gaming industry. I've personally seen enough culture bias and monotony of this nature in games to be very bored with it. Thankfully, there is a good chance people will simply not buy games that continue along the line of similarity. This is very much an innovation industry like that, and this may keep things interesting.
From a design standpoint, I must ask: if there must be religious/moral systems in gaming, then why not make them as diverse as the ones we are presented with in the real world? How about, instead of simply having "good" and "evil", having "orderly" and "chaotic", a Y/X axis scale that literature and fandoms have already begun to use?
Or better still, have a reading that shows what secular philosophy/religion your set of actions so far conveys (a kind of changable reading from gameplay history). For example, your character might visit one church and go save some people, this would make them read as that religion, but if they pray at different churches, that makes them a universalist. If they kill everyone in sight, they might be a nihilist. If they rebel against more than one government with different views, they become an anarchist. If they kill one man when they see his about to do something evil, they might be seen as a utilitarian. If they act selfishly, objectivist. Continue this around the many flavoured scale of world philosophies, and you have a powerful, diverse system that would keep players engaged for years. It's not a simple thing to code or understand. However, it is something that gaming sorely needs.
Such a reading could create complex factional consequences in a world-scale game, whereby people with similar "beliefs" (actions) will ally themselves to you, and others will slowly become enemies, neutral, or unsure (apathetic) as you establish yourself. This realism would actually teach people something about true consequences, rather than being, as many complain of moral systems in games so far, "preachy".
In literature, almost every philosophy has been given a narrative in some form. The same goes for film, though it hasn't existed for as long and hasn't covered as much yet.
Gaming, meanwhile, is new to morality and ethics. I think that there must be a push for diversity, not simply Christian morality, in games. Unfortunately, thanks to the extremity of possible decisions in most games with morality systems, they seem to have a fairly obvious, simple, Christian basis. This isn't always true; there are games like Masq, which show more than that and throw unexpected consequences in to make being "good" or "evil" less easy and certain. But in terms of the mainstream, there is very little in the way of risks being taken to do something interesting with this.
If we're going to have a lot more religious games, then they will depart much more completely from the simple idea of being fun or not fun. This is both a good and a bad thing for obvious reasons. I really hope that the good side of this consequence is emphasised and strengthened by pushing for diversity and not black and white decisions in games. The potential for the demonisation of any faith and prejudice is very strong - this could also be avoided if each game character still acts separately from their factions in one way or another as individuals.
Games like PeaceMaker seem to do things right. A few more games about reaching peace (through diplomatic means) rather than waging war would be a fantastic thing which balances the situation. And not just because they're good morally, but because such games improve the image of gaming itself.