Beginning with a system similar to D20 modern, the first place to start would be replace the combat system mechanic with an equally sophisticated alignment system mechanic so that you can conduct and be subject to 'spiritual warfare'.
Create a bunch of feats and skills designed to corresspond to the christian virtues, gifts, and teachings.
For instance, instead of 'dodge' and 'improved initiatve' a serious D20 'Christian RPG' would have 'gifts' like: 'Faith', 'Hope', 'Charity', 'Compasion', 'Soberity', 'Tongues', 'Prophesy', 'Holiness', 'Healing', 'Discernment', and so forth.
Anti-Feats and limitations would be very important to the game: 'Addictive Personality', 'Depression', 'Frivolity', 'Lazy', 'Short Temper', etc.
Instead of skills like 'pick pockets', 'tumble', and so forth, 'Christian heroes' would pour skill points into 'Evangelism', 'Teaching', 'Discipleship', 'Ministry' and so forth. Other tradiational skills like diplomacy, sence motive, perform, and heal would still be popular.
Alot of the game would focus on obtaining sufficient 'guidance' and 'violition' points to overcome obstacles faced in thier way and achieve the goals of their mission. Players would probably have less freedom to act compared to tradiational RPG's, and alot of the game would be trying to gain control of your character when faced with various 'trials' and 'temptations'. Failure on a trial or temptation check would result in your character either doing nothing, or worse yet doing something harmful to himself or to someone else.
One of the most difficult things about the game would be coming up with real challenges for the players, since most people know what they ought to do and would always try to do it in a RPG, but in real life people don't always do what they know to be right. (Thus all the rules limiting freedom of action). It would be a very hard game to DM and would cut a little too close to home for me alot of the time. Besides which, I'd feel very uncomfortable taking the role of the God as a DM.
You'd probably be better off using an arbitrary fantasy setting and introducing aspects of Christian morality, though as pervasive as Christian morality is in Western though I dare suggest you'd be hard pressed not to be influenced by Christian perceptions of good and evil.