The history of Reformed (Augustinian/papist) logic and practice does make sense, but only if you swallow its false starting point of Law.
If you believe that you are Israel...if you believe the "moral law" is still in force for faith and practice...and if you believe that you are in, or helping to bring in, the theocratic Kingdom of Christ, then it's a very small step to putting to death heretics (however you define heresy) if you have the power to do so, just like as happened under the Law.
That's how you end up with professing Christians today talking a lot about grace but defending legalistic, doctrine-based murder for whatever they define as heresy.