Get over yourselves
I'd say that The Register becomes more like the Daily Mail day by day, but that'd be an understatement, The Register nowadays really IS the Daily Mail in IT format.
Comparing the Cathedral situation to this one is rediculous, the Cathedral thing hadn't blown up until Resistance was already widely distributed to the public, this in contrast is a pre-release realisation of the problem.
I too am an atheist but I also have the ability to respect the fact that others think differently and have their beliefs. Bringing the whole "terrorist" thing into it is pathetic, there's 1.3billion muslims out there and not even a noticeable percentage of them engage in terrorist activities anymore than you might call atheists rapists because there have been some atheist rapists or than you might call christians paedophiles just because a few people are guilty of such crimes.
There is no special treatment of muslims here any more than if there had been something with racist, sexist or say homophobic undertones in the game discovered PRIOR to release. This is what companies do, because offending 1.3 billion people in the world is not good business sense, particularly when Sony are already struggling with PS3 hardware and software sales.
Yes I think the world would be better without all the problems religion causes but no, attacking it and calling favouritism when it's just good business sense really is not the way to reach that goal. If atheists continue to do what they've always done - be the leaders in science, many of the most intelligent people out there then that's how things will change. Stooping to the level of attacking religions when it's simply not merited is completely the wrong way to go about things and is exactly why we have religious extremists the people you're crying so hard about in the first place!!