The portrayal of religion by popular entertainment has long been a source of concern. Rarely has anyone gotten it right, even long ago, because it has been typical for centuries that the people involved in acting and putting on entertainment tend to be less religious than the general populace. When religion isn't misunderstood or oddly portrayed by an outsider, its insulted, mocked, or belittled. Especially lately its gotten pretty standard to shower spite and misery on any Christian in any popular media with a few very stark exceptions which only serve to prove the rule.
Video games are no exception here. Recently Gamespot posted a video examining how religions are portrayed in video games. Aside from the quasi religion of the Jedi invented by borrowing from lots of sources (mostly Buddhism), religion is largely ignored in video games.
There have been examples, such as El Shaddai, Dante's Inferno, and Messiah. However, those are more settings and premise based and don't really deal with religious issues or theology, as the narrator points out. Most games just have an atheist perspective. People aren't religious, or anti-religious, they just don't bring up the subject and it doesn't exist in the world. Avoiding the topic of religion helps avoid controversy and annoying buyers, so game designers just don't touch the subject at all.
A few do, however. Bioshock is largely built around a rejection of religious authority, but reasonably does have people seeking something beyond their lives, particularly during war. And most fantasy games have some sort of religious presence, such as the Elder Scrolls games which have a fairly well fleshed out system of good and evil, gods, blessings, priests, and so on. Others tend to view religion in their setting as more a prop for types of characters to have power.
Interestingly enough, in the 3rd age after Oblivion, Skyrim is set when a human that became a deity has had his religion banned and a group is hunting down and slaughtering all worshipers and leaders of the former religion. And the game series Mass Effect has always had religious aspects, speculating on how they might change with interstellar travel and alien encounters.
Islam is rarely portrayed unless the setting is one where the religion is practiced. Assassin's Creed, for instance is set in the Middle East, as is Prince of Persia, but the religion is a background thing, like the decor or plants. It just exists as something you move past, not interact with.
Part of that is because of the concern with enraged psychopaths who hack heads off and riot burning down things when Islam is mentioned. Often, the bad guys are Muslim, such as in recent Counterstrike which is Americans vs Terrorists.
The interview with the Muslim Tamoor was pretty useful because he's a Muslim and thus most people on the left will find him less intimidating and culturally problematic than a Christian. He says basically what most Christians would say: just include us as a normal part of the world. Some good guys, some bad, just a part of people's lives. Make your characters have more depth by giving them faiths but don't make that their cookie cutter defining characteristic. Don't make "Bob the Christian", make Bob the cautious grocer who collects old magazines as a hobby and happens to be a Christian.
I did find it interesting that he felt the need to identify Islam with Arabic culture, however, when Christians view their faith in terms of the religion its self, not any particular cultural setting. We don't think it should look and feel Roman, for instance. I think perhaps when Islam can get away from that tendency it will make a big step toward moving away from the crazy murderous types.
The piece went out of its way to note that most people in a faith aren't like the ones that get quoted in the news - Christian, Muslim, Hindu, or otherwise. And that's generally true, you can't really judge a religion as a whole by the crazy guys that get on camera. Media has a lot of biases, but the biggest one is spectacle, they love a crazy guy who looks interesting and gets your attention. And the worse they can make Christians look, for instance, the happier a lot of them are.
So my advice for game companies (as well as other entertainment media) would be this: don't let complaints about your product force you to make changes unless they are reasonable and objectively just criticisms. In other words, don't change your game because a small group of people get upset you used a line from their holy book in a song, but do change it if a group of people are annoyed that you only and go out of your way to portray them as bad.
Because like it or not, religion is a very powerful, interwoven and inextricable part of all our lives, history, culture, and future. Leaving it out of your work makes your setting seem sterile or unnatural, and deliberately so.