One of those things that is hard to write about is religion. There is arguably no more contentious subject than religion, and for all of the right reasons. There is no question that I consider myself a deeply spiritual person, and that is just part of who I am. However, I do consider some people, even those that share my same faith, complete morons; ask me about the WBC sometime. At the same time, although I consider some atheists complete idiots, and I make no bones about lack of respect for Penn Jillette and Bill Maher, I do tend to respect atheists, especially those that respect me. Nonetheless, it doesn't mean that either side should completely rule a comic.
The problem is that we define ourselves by our beliefs, be they as religious or atheist. Admittedly in some cases a person's spiritual beliefs aren't going to matter; there are a number of great comics where the beliefs of the individuals doesn't matter and would actually get in the way of the comic, so don't feel like you need to feature it. This is not to say that people are amoralists or anything like that, just that the writer didn't feel like bringing religion into the situation. That's fine.
On the other hand, you have those comics where the pendulum swings too far one direction or another. Either it is extremely atheist and religion is a corrupt joke, or spirituality reigns and atheists are idiots. In both cases the problem is that, well, any extreme position is a bad position. I don't respect fanatics of any faith, including atheism; fanaticism tends to blunt any point that it's trying to make. From the atheist perspective, slapping down religion is bad because religion has, on the whole, done far more good than bad. From the religious perspective, religion does need to be slapped down and on a regular basis. In both cases, attacking just for the sake of proving your side is better is going to annoy some readers, and that limits your audience. [Oh, right, this is a marketing blog, too...] So if you are taking an absolute position, realize from the beginning that you had best be doing it right, or forget it.
By right, I mean recognize that both sides are essentially correct. I'm not saying that religion not get slammed; some of the best villains have been religious zealots or those that have used their position for power; how doesn't hate Cardinal Richelieu? But, if you are going to have an evil church, show that there is a reason that people follow the church, and not just because they have large weapons pointed at them. There are a lot of good reasons people believe in a higher power, and not all of them are just because they believe that God is the bestest person ever; you would be surprised how many scientists like His works.
In general, any organization is going through periods where it does its job right and periods where it doesn't; there is no reason that this cycle should not apply to a fictional religion any less than in real life. Another thing to keep in mind is that ambitious people love corruption; it means that there are plenty of chances for advancement, as well as ways for them make their own opportunities. This means that there are two fun situations that can be the case: Either the local corrupt chapter is aiming for the top, or that the top is corrupt and the local chapter is ready to force a change. There are other permutations, but these are your best options.
On the other hand, there is no reason that atheists should be portrayed as morons, unless you are making a point about religion in general. In that case bear in mind that the idea that a leader does not necessarily represent his flock; sometimes the leader is just the one that get the others going in the same direction. The basics here are that atheists make easy enemies to simplify for the purposes of having an enemy, but generally you just want the leader to be an idiot and his followers are just following his lead. This brings up the question of why they are following his lead, and a church that has been downright silly. In this case you have a great set up to poke a little fun at both sides, and you should take advantage of it. If not, your comic will suffer for only considering one side the better one.
This pretty much applies to any comic that has two sides; a fair perspective on both sides will bring a lot to the comic. Don't get me wrong; I love an enemy that is plain evil, and that's why I like using demons and devils as enemies. But I do throw in the occasional good devil just to mess with people, and the bad-alien-turned-good should be a familiar trope. So have some fun with your bad guys, and don't make them too one-dimensional...