Jonathan Rowe has an interesting post on the history of religious freedom at "Positive Liberty." In the process, however, he implies some things about Thomistic natural law theory that are not quite right. He says, "The 'old' (Thomist) version of the natural law justified such things as slavery and burning heretics at the stake and knew nothing of the concept that men existed in a 'state of nature' and possessed unalienable natural rights."
Burning heretics at the stake is not justified in Aquinas by appeal to natural law, but difficult as it may be for us to wrap our post-medieval minds around the idea, by appeal to public safety: if any capital punishment is justified, it must certainly be justified for those who, having previously committed themselves to the saving faith, have broken their obligations (e.g., baptismal vows) and promises and are leading the community to eternal damnation, and refuse, after several opportunities, to repent. Aquinas explicitly denies that slavery is justified by natural law, since he holds, as indeed was traditional, that all men are equal by nature; slavery only arises through positive law. It is true that he does allow it to be consistent with natural law if it is imposed by positive law as punishment for crimes, and if it does not violate the slave's rights to food, sleep, marriage (or celibacy), raising of their children, and religious worship (and anything else that pertains to natural law); but it's worth remembering that when we make prisoners do community service we are imposing slavery (servitus) in Aquinas's sense (i.e., forfeiture of the free disposal of one's person as a punishment for a crime or by contract -- Aquinas's term can, but does not always, include hired domestic service). However that may be, natural law was not, and could not, be a justification for slavery, because slaves are not subject by nature.
As to unalienable natural rights, we can set aside 'unalienable' (since it just means 'not able to be transferred') and ask about natural rights, since anything natural in a Thomistic sense would be unalienable. Aquinas does, in fact, hold that we have natural rights; they are things that can reasonably be expected as a matter of justice (for Aquinas 'right' is synonymous with 'just'). When we engage in just action we are rendering someone his or her right. Where he falls short of Jefferson and the like in this regard is not in lacking such a notion but in not developing this in the direction they do. It's also true that natural law theory has no state-of-nature notion; but it's also true that by the time of Jefferson et al. the notion of a 'state of nature' had begun to fall out of favor: Hume, for instance, attacks it as an absurd fiction.
