Trying not to repeat everyone else here, so here's one of those 'similar experiences' things.
I work designing stuff(banners to brochures to logos) for a private company whose owners are very religious. More than once I've been asked to do 'spreading the Word' type pamphlets for many many different churches on many occasion, and, while not an atheist myself, a lot of the Messages I've been proof-reading and spell checking and assembling in exquisite design I don't approve of(funny story, I actually let some of my own beliefs slip at work in casual off the clock convo and immediately got a talking to about devil-worship; fun times). BACK TO THE POINT, I do these designs anyway, and I give it my best shot. I don't see this as whoring, and I'll admit, this could be just rationalization, but I see it as thus:
If I seek to be a professional designer, then a part of being professional is removing personal beliefs from the job and making something that stands out. Why? Because the customer is seeking a service, and I've been tasked with making whatever message they want get out there above everyone else's(kind of tough in Va too; churches are a dime a dozen). So, each one of these jobs are a challenge to remain detached and focused and make the best looking pamphlet imaginable despite belief difference.
With that in mind, no, if you put this on your resume, I doubt it would reflect on you poorly. If anything it could show how well you can work on a project despite being a subject you're not 100% behind. What I should have simply said, if you can muster the gumption to stomach the rhetoric, do it. If you can't, no regrets, no worries, you'll find other work. Don't push yourself if it's causing a big battle with you.
I reject your reality and substitute my own.