"(We still want something that's bad for us, so alcohol is the exception for historical reasons), but (for probably misguided utilitarian reasons, we don't allow all sorts of drugs)."

or

"We still want something that's bad for us, so (alcohol is the exception for historical reasons, but for probably misguided utilitarian reasons). We don't allow all sorts of drugs."

The former suggests we prohibit drugs for utilitarian reasons, misguided but utilitarian nonetheless, the latter seems odd by itself?