Hmm....
I find it amusing that anyone could possibly be offended by this, and I'm religious. It seems like you're attacking a personality that exists among religious types, not quite the religion itself.
For example, your atheist character is witty, logical, and seems to be a nice guy, but your christian character is stupid, obstinate, and he's got a funny accent. Like when he says, "Ah luk after MAH wimmens," i just bust out laughing, because you've got to be a bit more subtle than that! I mean really, why not say, "I think Christians are inherently illogical and stupid!" That's the only complaint about this whole short, the way that your characters are so...just so typical.
The atheist is just so likeable, and the Christian is just so annoying. If you're implying that there are these types of figures in Christianity and atheism, I'm with you, man, all the way. But if you're implying that all religious folk are warmongerers and ignorant, then I'd say that you must know some (pardon the profanity) godawful people. '_^
Could you imagine it, though? The President tells the public on March 19, 2003 that "we have evidence to believe that Iraqi men are mistreating their women, and we have offered sanctions and diplomacy, but they still mistreat their women, and so we had no choice but to bomb them."
"Erm, Mr. President, could you elaborate on the evidence?"
"Well, John, they're Muslims."
"Oh, I see. That...explains it."
Certainly just as factual a reason as any that have been given supporting this war. XD
In conclusion, very well thought-out, not offensive at all, and keep it up! You've got my support, I, a practicing Muslim. All I've got to say is, don't think so bad of us. I'm not sure which religious person inspired your Christian character, or if there was any person at all, but we're not all like that. Most of us aren't. Honest to God.