Yeah, 12-step programs are very problematic that way. The whole process involves surrendering to your higher power ... which is a major issue for atheists. There's the classic line, that your higher power could be a tree or a rock, which is really freaking stupid.
There are a few groups like Secular Sobriety, but they don't have the same kind of coverage. Since religious groups push 12-step programs, it makes it easier for them. You can find a church that's willing to host a 12-step program in the middle of freaking nowhere.
I don't know what other groups might be run by other secular organizations. A Google search for "Secular Sobriety" or similar search strings should turn up a couple of others. I know they've mentioned a few other groups on The Atheist Experience, but I can't remember any of them.
Heh, same sort of shit from AA, as I've heard from other religiously-themed sources. I've been to a few religious services which are supposedly addressing atheists and speaking to them. They're always ... pathetic isn't a strong enough word.
The only thing that I've ever taken away from a talk about atheists, by religious people, is that they have no clue what atheists really are or what they think.