Dragon Age, while easy to dismiss as 'just fictional religion' (which you said you didn't want), I think has a great deal to add to discussion beyond their religions just being plot point tools. Religion to the people in dragon age isn't just one line throwaways or limited to just influencing fanatics (though there are certainly those as well): there are a great deal of characters (background and major) wherein you can see the influence Religion has on their thinking, their morality, and their decisions, without being a two-dimensional ONLY factor informing their behavior.
It even does one better than that with multiple, complete religions (ie. one isnt the overshadowing 'good, proper' religion while the others barely get any screen-time and are designated-villains) and exploring how they interact, similarities and differences, and made all the better with both sides having both their saints and their atrocity-perpetrators. There's conflict of course, but a lot of times characters who while fervent in their own beliefs aren't determined to start a fight just because they're being asked to cooperate with someone whose views aren't theirs; once again depth being added by some characters being able to put aside such differences, while others can't, rather than a black-and-white Aesop about cooperation.
And then you have the biggest conflict involving religion in the game: Mages. even Mages themselves can't agree if they're being punished for some transgression against their god, are just people in unique circumstances, or are empowered to be the Ubermen of their world. The biggest show, in my opinion, of commentary on religion involves the mages; the Templar who control them are a deeply-religious sect, but even beyond the Templar the rest of the population buys into religious excuses for the fear that motivate the more terrible of practices the Templars use to dominate Mages. Again, made all the deeper by setting a scenario where what the Templars are doing may indeed necessary evils given the powers of an out-of-control mage, or may even just be making things worse, as Anders suggests by pointing out that the Circle-system creates a mindset of fear and suppression and loathing that causes the Mages to seek the power to break that oppression in the first place. But either way Religion, while itself not responsible for the acts committed by the Templar is nonetheless the shield they use to shut down discussion of the matter, a sadely accurate commentary on the real world past and present as well.
