Hi, I'm Dan. And I'm a 12-stepper. LOL
I don't buy into a lot of religious crap. I was abused by a minister, and I don't believe that because you carry a Bible around or wear a collar that you're automatically trustworthy. In fact, I have a pretty hostile outlook toward most organized religion in general.
Having said that, I don't find that this is really an impediment to following the 12 steps. Even though a lot of 12-step groups meet in churches, the steps themselves require an acceptance of a higher power, however you define that. For me, that has never meant a God, as defined by any organized religion. It has meant the acceptance that there is something that keeps this world spinning, that pushes us from birth to death, that keeps the sun shining and the trees green, etc. That makes this a living planet rather than just a lump of atoms. I don't know what it is, but I accept it's there and I can entrust my own life to this higher power. In fact, can is the wrong word. My life is in the hands of this higher power because I have no choice about it.
I have occasionally run across 12-step meetings where the language of the meeting is more specific, usually referencing Jesus or a Christian god. If it's one or two people in the meeting giving it that flavor, I apply the old saying: Take what you want and leave the rest, since they should feel free to embrace a higher power of their own choosing. If the whole group has adopted a Christian-only outlook, I move on, since they've moved away from the spirit of 12-step recovery, which does not support this type of exclusive outlook.
If I were in your shoes, I'd attend a couple meetings and/or arrange to talk to members and ask them about your concerns. I'm sure there will be people who are well aware of the issue and can give you a quick read on the group. You might ask them how Muslim, Hindu, Jewish, Buddist and aethiest members operate within the group and see what answers you get.
The bigger problem I have with 12-step programs is that they are in my experience basically behavior modification programs that can fall short of really helping give someone a full life. For me, recovery from sexual abuse requires work on issues that are specific to me that don't fall neatly in the 12-step framework. So for me the 12-steps make for a good foundation to recovery. But they do not get me all the way there.