Being willing to alter your deepest held beliefs predisposes you to altering other things about your life, from big things like moving across town to small things like taking a lunch break at a different time.
There's also a social element that I think is hard to reproduce in a secular context. Convincing a bunch of adults to coordinate their schedules is much easier if they believe that they will go to heaven if they do so. Furthermore, you already have a public building as a location to hold meetings. Hell, even the architecture of a lot of churches is awe-inspiring. They're physically designed to be these places where you come to terms with your faults (sins) and begin to deal with them. Of course, that also means that their design is religious, with religious iconography in the stained windows and on the walls.
I'm not sure how standard AA can help an atheist, since about half their 12-steps mention god, submitting to a higher power or praying. If atheists say it helps them, I believe them -- who am I to doubt it? But I don't understand the principle at work.