I'd just like to point out the error in the argument stating it's hypocritical to have a problem with blasphemy but tolerate killing in games. Violence is simulated, pretend, not real. You can't have pretend, or simulated blasphemy. If you shoot a pixel at a pixel you didn't hurt or kill anyone, but if you blaspheme in a game you most certainly have blasphemed for real (not necessarily the player, though...)
Ultimately, what's more important is what you make of it and the objective of the message. In this case, I believe the blasphemy is just a cheap story tool that the writers used to set the scene. But... it's not necessary to freak out about this sort of thing because A) your reaction isn't doing anyone any good, and you're not making the world a better place by freaking out, and B) you're just making yourself look like a nutcase.
Religious people are looked down on enough already, no need to make it worse.
Still, it was a good move by Valve to refund the user. I wish businesses in SA would provide this kind of service and show such a strong customer focus

they may have lost a sale but they kept a customer happy