My apologies for my harshness, but wow, those links were horrible. The non-video links are really the most vapid kind of argument-free partisan blogspam, filled with guilt-by-association logic, and overstating their conclusions.
However, by walking the link-graph for a while from one of your links, I found this, which seems to contain some useful detail, and seems to agree with the bias of the articles you linked: http://www.morerevealed.com/library/coc/chapter7.htm It claims that the evidence is pretty terrible overall, but there is some evidence that AA is worse than no treatment. Hmn.
I wasn't able to bring myself to read the terribly-presented websites of the suggested non-religious alternatives. Ugh. Since you claim there are "more effective, non-religious, evidence-based" alternatives, could you point to some evidence? In particular, evidence of "more-effective" and "evidence-based"? That'd be super super useful to people!
And the P&T bit is almost entirely rhetorical dirty tricks. You can pick any minute of it where Penn is speaking, and find several logical fallacies and rhetorical innuendo. (The interviews vary greatly in logical clarity.) Though I agree with one thing Penn is ranting about: courts (or employers) mandating AA attendance is highly objectionable, on several levels.
I'm very interested in this subject for two reasons; I'm a devout atheist, and I've seen an enormous improvement in the life of a loved one directly chronologically following that person's involvement with AA. It's just a single anecdote, and anyway perhaps there was no causation in this correlation, but it has definitely piqued my interest in whether AA can work, and how, and why, and what it has to do with religion.
I've found that when one attends an AA meeting, one meets a lot of people who claim to have been profoundly improved by AA... but I realize that maybe that's just because the success stories stick around and populate meetings for 4 or 40 years. Maybe it works really well for some, but maybe the success rate is terrible.
Successes notwithstanding, even if they might be rare (or common! I dunno!), I would agree there are many valid criticisms about AA. As one of P&T's interviewees points out, they resist change, and have no feedback mechanism to improve themselves. There are advantages to dogmatism, but disadvantages too. But I will say that, at least in the lefty-leaning SF Bay area, it is quite possible to be an atheist at AA. But it's still America, so if you randomly sample the population, you're gonna find a lot of professed Christians, and so an atheist at AA is going to need to have considerable tolerance of other people's (crazy wrongheaded) opinions. I would say that it's not a religion, but it is a club full of religious people, talking about things that they think are related to their religion. Maybe the SFBA is atypical.
I haven't experienced chemical addition personally, and I don't know anything about the effectiveness of other programs, but if there are atheists out there avoiding AA-like programs for religious reasons and would like to talk about reconciling those things, my email is in my profile.