I'd like your input...

What is the offensive part?

Also, who are you worried about offending? Will reasonable, informed people by offended, or are you imagining the people who engage in evolution/creation debates online? In the latter case, that's just a stratum of society who enjoy being offended regardless of their political or religious affiliations.

Personally, the thing I find most offensive about "religious" type stuff is when the creator diffuses misinformation owing to their ignorance of the subject matter. This is something true of both secular and non-secular materials. I'm tired of asexual Puritans, evil crusaders, and pop culture depictions of Galileo's trial. Damn people, you don't need a degree in theology, but at least take a college level history course.

I'll be more than happy to see if it's offensive. I have a similar concern about my Biker Bar Brawl game. I'd like to see how you handle it. You're not going to offend me. I can see if my wife would want to look at it too. She is generally more sensitive toward religious, cultural and racial matters.

Just wanted to mention quickly that i enjoy your artwork for Splat, the duck and diver. As for a game of conflict of religious beliefs, i find it odd to be offensive if you would recreate a conflict of faiths that have occurred in history.
But as you have stated your "factions" are fictitious it would seem to be less of a problem, but just as an opinion. It doesn't seem that your idea is telling someone their belief is wrong or that they should have malice toward others. As Soulfinger suggested, there will be those who will look for a fault to be offended.

I was giving this topic some thought. One option is to make all of the factions insects while retaining all of the religious trappings. The use of animals and insects in allegories is well established and generally goes over the heads of people who are readily offended (at least until someone else instructs them to be offended). It makes for a fun theme too since the players can represent the hive minds that are worshiped as gods, which also physically influence the thoughts and behaviors of their followers. Playing around with the symbolism, parallels, and metaphors could make for a fun theme.

Personally, I'm a huge fan of Gene Wolfe's Book of the Long Sun, in which a holy man communes with a god who exists outside of his people's established pantheon. This is a huge spoiler for anyone interested in reading the series, but it turns out that the human beings are on a giant spaceship and all of their gods are computer programs, the digitized personae of the ruling family who dispatched the ship. These are themes explored by other sci-fi authors, but none quite so elegantly as Wolfe. I think it would be a great setting for a game.

Anyways, you would be quite fortunate to provoke people with your title. That's free advertising from people who weren't going to be your customers anyway. Religious fundamentalists and militant atheists are like a revolving door. The more one half of that group denounces something, the more the other half will sweep around to embrace it. Ultimately, it's the same market segment, and the controversy serves to provide exposure to more level-headed consumers.