I would agree as well - these people are trying to major-ly change their lives, let them smoke!! Besides, there is a cultural aspect as well: the guys hang outside together, bum smokes from each other, at AA and NA meetings, coffee and cigarettes are actually a pretty big part of the scene. Not condoning, but in his time he will quit those things too. Mine put down the cigs a few months out of treatment.
Your son is likely frightened, and I don't blame him. This is huge. Personally I don't think 60-day programs are enough for people who are hard-core; you have time to get clean and be introduced to new tools, but not long enough for indoctrination. I would encourage the longer one, but it is of course his choice.
Treatment facilities have different details but core concepts are the same (unless you go to a "Health Realization" type program)
It works if you work it.