Extract from Father Terry’s Verbal Conscience website (http://www.frterry.org), Handout 126
Theological justification for the repression of heretics
With regard to heretics, two considerations are to be kept in mind:
1. On their side.
2. On the side of the church.
1. There is the sin, whereby they deserve not only to be separated from the church by excommunication, but also to be shut off from the world by death. For it is a much more serious matter to corrupt faith, through which comes the soul’s life, than to forge money, through which temporal life is supported. Hence if forgers of money or other malefactors are straightway justly put to death by secular princes, with much more justice can heretics, immediately upon conviction, be not only excommunicated but also put to death.
2. But on the side of the church there is mercy, with a view to the conversion of them that are in error; and therefore the church does not straightway condemn, but after a first and second admonition, as the apostle tells us. After that, if he be found still stubborn, the church gives up hope of his conversion and takes thought for the safety of others, by separating him from the church by sentence of excommunication, and further, leaves him to the secular court, to be exterminated from the world by death.
source: Thomas Aquinas, Summa Theologica, IIa, IIae, 11, art.3.