Aaron,
The ruling (and similar previous rulings) says the government can't mandate or compel offenders on supervision to attend religious self-help groups like AA or NA, but it doesn't say they can't be part of an offender's treatment plan if the offender is inclined to attend them. I usually suggest that the person attend a community self-help group of their choosing, such as Alcoholics Anonymous, Narcotics Anonymous, SMART Recovery, or any other group that might be offered through a local community center. I have yet to actually meet an offender who did not want to attend 12-step meetings on religious grounds. If your agency offers in-house groups, you have greater assurance that the offender actually attended.
SMART recovery groups are not widely offered and usually require a higher degree of literacy and cognitive ability than many offenders possess, but they are a nice option. I have found meetings and information on www.smartrecovery.org. Rational Recovery does not actually have meetings anymore. Rational Recovery was billed as a secular CBT alternative to 12-step groups, but the founder ultimately turned it into his platform for a diatribe against 12-step groups.
I see that it's been awhile since you posted your question, so you have most likely discovered all of this by now. If not, I hope this helps.
JLB