The article is a pretty good summary of the sad state of alcohol and drug dependency treatment in the U.S. The prescription is always abstinence, and almost universally any suggestion that moderate drinking might be possible for some is met with scorn and anxiety.
My objections to AA have little to do with their mention of God. I am christian, so obviously that is not a problem for me. I will say that AA theology is awful, basically implying that salvation comes from sobriety, but worse is that it actually indoctrinates many with ideas that hinder their ability to recover from addiction. Regardless of whether or not you believe the way I do, I hate to see people needlessly suffering from this illness (or perhaps, this group of related illnesses), yet the conclusion I came to after 25 years of involvement with them is that AA more often than not prolongs suffering.
I am not saying that naltrexone or any other drug is the magic bullet, but I am certain that it is well worth investigating alternatives to AA. If you or anyone you are close to needs help, please take the time to explore all the options. There is so much snake oil in this area that it can be difficult to know which way to turn. It is worth the time and effort it takes to find the right treatment, and if it is successful, it is probably even worth the inflated cost of said treatment.