Someone involved in the field told me that he was counseling a public figure in dealing with am addiction, and the person wanted to find a 12 step group where he would not be recognized. He drove some distance to a program in the basement of a church, and when he walked in, another frum person was sitting there...
Also, if the program is happening in the social hall or basement of a church, and is sticking to the program, there is certainly no problem in going (although an addict will use any excuse). But some churches have programs that are explicitly Christian but loosely based on the 12 steps, and that is Assur. In other words, not all "12 step programs" are really doing only the 12 steps.