In our present age, the Church's beliefs about the functions of the civil government are heavily influenced by relativism and to a lesser extent, by the Voluntaryism of Roger Williams' Rhode Island. However, in many of the Reformers' systems of thought, the Church was not viewed as entirely separate from the civil authorities, nor were outright heretics viewed as simply another denomination. Kings and queens, as in Is. 49:23, were the foster fathers and nursing mothers of the Church, destined to help Her spread Her doctrine over all the earth by protecting correct religion.
Moreover, modern evangelicalism has chosen to see the relationship of Old and New Testament as fundamentally discontinuous. The Reformers saw it as more continuous. The model for Church-State relations was not to be found in Church's status in the first century as a persecuted subculture. The model for Church-State relations was found in the manner in which the civil authorities of Israel interacted with the Levites of the temple. The judges and kings of Israel supported the Temple and its work. They also were under orders by the Law of God to stone to death anyone who had been established in a court of law as a murderer, a blasphemer, a homosexual, a bestial, or a sorcerer. Consequently, most of the Reformers saw it as the civil magistrate's duty to do the same for the Church.
We must remember that Calvin himself, and his church in Geneva, killed no one. It was not, as some people like to paint it, an instance of murder. It was an instance of civil justice, carried out by the Genevan City Council. By attacking the Trinity, Servetus had declared himself an enemy of that God upon which the State relied for its authority. To the Reformed mind, this was the same as treason against the State.
We are modern people, influenced by Enlightenment rationalism in ways we often do not perceive. Do not let your modern sensibilities cloud your judgment of what was ultimately a biblical response to Servetus and others like him.