Wow, he doesn't seem like a first amendment kind of guy.
He isn't stating, "this is what I believe ought to be done."
He is stating, "this is the argument that says that heretics must be executed."
Aquinas actually states right at the top of that passage:
It seems that heretics ought to be tolerated. For the Apostle says (2 Timothy 2:24-25): "The servant of the Lord must not wrangle . . . with modesty admonishing them that resist the truth, if peradventure God may give them repentance to know the truth, and they may recover themselves from the snares of the devil." Now if heretics are not tolerated but put to death, they lose the opportunity of repentance. Therefore it seems contrary to the Apostle's command.
He also goes on to explain that heresy isn't holding contrary opinions to the Church, it is both expressing those opinions and rejecting the authority of the Church. The second part is crucial. For he says that righteous men can disagree while heretics must have the will to split and form their own groups apart from the church.
He even goes on to argue that heresy has nothing to do with unbelief, because unbelievers cannot be heretics, and that the sin comes from pride and not lack of understanding. Heresy is found in all religions, hence it stems from a failing of the flesh, not of the mind.
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