I like to think that if you can poke holes in your own religion/beliefs, then it's easier to come to terms with it. I come from a family of religious folk, many of them working with and for the church as pastors and the like, but we also don't mind making a joke about how Jesus' hands could pass for plug piercings nowadays (what with the holes in his hands), or how it would be super awkward for Abraham and Isaac to sit at the dinner table after his dad was ordered by God to kill him.
And I'm not even religious, I'm strongly atheist (as far as I know, the only one in my rather large family who is). So when I read this:
In my comic I like to take jabs at atheists in the same way (not planning to do it often).
then it seems you're sort of creating a double standard/being a hypocrite, you know? Buuut that's just me.
Just another thought as well:
if this is meant to be a sarcastic joke, well done, i chuckled lol if not, you might be in the wrong business ;O Especially when it comes to Christianity and comics coming together as one - the only time Christian comics have succeeded is when a.) they were very unique and interesting takes on old stories, or b.) they took the comedic route, which sort of makes you appreciate the religion more in a weird sort of way.
Can an enlightening comic be done well? One that teaches people about Christianity and doesn't fall into any of those two categories mentioned above? Possibly, but you really have to know what you're doing, and you can't just shoehorn it in or spoonfeed it to people. I've read comics like that before, and they're more damaging to the religion than helpful, as they just paint their own faith in a negative light that screams, "LIFE WILL BE TERRIBLE FOR YOU IF YOU DON'T JOIN THE CHURCH, YOUR FRIENDS WILL BETRAY YOU, YOUR WIFE WILL DESERT YOU, YOU WILL DIE OF SICKNESS, AND YOU WILL DIE ALONE." (seriously, I've read comics like this, they are terrible. No beating around the bush with this, they are the worst things I have ever read and they sound more like propaganda from 1942 than they do enlightening stories about a particular faith.)
But then again, you said that you were doing this for fun, so hopefully it shouldn't come to that 
If you are doing this for fun though, then you should understand my earlier point about the comedic side of things - there's a light side to everything, even religion, and finding it can make you appreciate it more so long as you go about it the right way. We all know that the creator of comics like Happle Tea could have painted those religions and mythologies and such in a much more negative fashion, but they took the high road, made a joke that everyone could get with basic Sunday-school understandings of the religion, and for some strips, they're even educational - I would have never have guessed that Zeus was a promiscuous womanizer who slept with practically every woman he laid his eyes on had it not been for finding the strips from Happle Tea that touch on it (and they do it hilariously by the way). And you know what? It makes me enjoy and read up on those original stories of Zeus even more, and the same goes for the Christian ones, because despite poking fun, they're still quite accurate, for the most part, in a comically literal sort of way.
