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Even if you’re a Protestant who doesn’t accept the magisterial authority of the bishop...You can decide whether you think Pius is right both to emphasize that Christ’s “kingdom is spiritual and is concerned with spiritual things” and yet still has some authority “in civil affairs, since, by virtue of the absolute empire over all creatures committed to him by the Father, all things are in his power.”

Oh, you mean the pope has authority in civil affairs. Yes, there are many here I perceive who long for a Catholic monarchy and the good ol days of the Inquisition and all its means, and thus silence all us who expose and reprove her fallacies:

Q. 539. What do we mean by the "temporal power" of the Pope?

A. By the temporal power of the Pope we mean the right which the Pope has as a temporal or ordinary ruler to govern the states and manage the properties that have rightfully come into the possession of the Church.

Q. 540. How did the Pope acquire and how was he deprived of the temporal power?

A. The Pope acquired the temporal power in a just manner by the consent of those who had a right to bestow it. He was deprived of it in an unjust manner by political changes. http://baltimore-catechism.com/lesson12.htm :

Pope Pius IX, The Syllabus (of Errors): "[It is error to believe that] The (Catholic) Church has not the power of using force, nor has she any temporal power, direct or indirect." Section V, Errors Concerning the Church and Her Rights, #24. (http://www.ewtn.com/library/PAPALDOC/P9SYLL.HTM)

The penal jurisdiction of the medieval Church included, therefore, first the merely ecclesiastical offences, e.g. heresy, schism, apostasy, etc.; then the merely civil offences; finally the mixed offences, e.g. sins of the flesh, sacrilege, blasphemy, magic, perjury, usury, etc. In punishing offences of a purely ecclesiastical character the Church disposed unreservedly of the aid of the State for the execution of the penalty.

The Church has the right, as a perfect and independent society provided with all the means for attaining its end,...the right to admonish or warn its members, ecclesiastical or lay, who have not conformed to its laws and also, if needful to punish them by physical means, that is, coercive jurisdiction. — Catholic Encyclopedia Jurisdiction

Pope Innocent III, Cum ex Officii Nostri of 1207: In order altogether to remove the patrimony of St. Peter from heretics, we decree as a perpetual law, that whatsoever heretic, especially if he be a Patarene, shall be found therein, shall immediately be taken and delivered to the secular court to be punished according to the law.

All his goods also shall be sold, so that he who took him shall receive one part; another shall go the court which convicted him, and the third shall be applied to the building of prisons in the country wherein he was taken. The house, however, in which a heretic has been received shall be altogether destroyed, nor shall anyone presume to rebuild it; but let that which was a den of iniquity become a receptacle of filth. Moreover, their believers and defenders shall be fined one fourth part of their goods, which shall be applied to the service of the public. — Cum ex Officii Nostri Pope Innocent III, 1207, Inquisition, by Edward Peters, p. 49

Pope Innocent IV, Ad extirpanda:

(25) Those convicted of heresy by the aforesaid Diocesan Bishop,surrogate or inquisitors, shall be taken in shackles to the head of state or ruler or his special representative, instantly, or at least within five days, and the latter shall apply the regulations promulgated against such persons.{7} (26)The head of state or ruler must force all the heretics whom he has in custody,{8} provided he does so without killing them or breaking their arms or legs, as actual robbers and murderers of souls and thieves of the sacraments of God and Christian faith, to confess their errors and accuse other heretics whom they know, and specify their motives, {9} and those whom they have seduced, and those who have lodged them and defended them, as thieves and robbers of material goods are made to accuse their accomplices and confess the crimes they have committed.

Canons of the Ecumenical Fourth Lateran Council (canon 3), 1215:

Secular authorities, whatever office they may hold, shall be admonished and induced and if necessary compelled by ecclesiastical censure, that as they wish to be esteemed and numbered among the faithful, so for the defense of the faith they ought publicly to take an oath that they will strive in good faith and to the best of their ability to exterminate in the territories subject to their jurisdiction all heretics pointed out by the Church; so that whenever anyone shall have assumed authority, whether spiritual or temporal, let him be bound to confirm this decree by oath.

But if a temporal ruler, after having been requested and admonished by the Church, should neglect to cleanse his territory of this heretical foulness, let him be excommunicated by the metropolitan and the other bishops of the province. If he refuses to make satisfaction within a year, let the matter be made known to the supreme pontiff, that he may declare the ruler’s vassals absolved from their allegiance and may offer the territory to be ruled lay Catholics, who on the extermination of the heretics may possess it without hindrance and preserve it in the purity of faith;..

St. Thomas Aquinas (13th century).

there are unbelievers who at some time have accepted the faith, and professed it, such as heretics and all apostates: such should be submitted even to bodily compulsion, that they may fulfil what they have promised, and hold what they, at one time, received". — Living Tradition, Organ of the Roman Theological Forum, http://www.rtforum.org/lt/lt119.html

“[It is error to believe that] Hence it has been wisely decided by law, in some Catholic countries, that persons coming to reside therein shall enjoy the public exercise of their own peculiar worship.” -- Allocution "Acerbissimum," Sept. 27, 1852. Pope Pius IX, The Syllabus (of Errors), Issued in 1864, Section X (http://www.papalencyclicals.net/Pius09/p9syll.htm)

"....Constitutions can be changed, and non-Catholic sects may decline to such a point that the political proscription [ban] of them may become feasible and expedient. What protection would they have against a Catholic state? What protection would they then have against a Catholic State? The latter could logically tolerate only such religious activities as were confined to the members of the dissenting group. It could not permit them to carry on general propaganda nor accord their organization certain privileges that had formerly been extended to all religious corporations, for example, exemption from taxation. [But] the danger of religious intolerance toward non-Catholics in the United States is so improbable and so far in the future that it should not occupy their time or attention." — The State and the Church (1922), pp.38,39, by Monsignor (and professor) John Augustine Ryan (1869–1945), imprimatur of Cardinal Hayes (http://maritain.nd.edu/jmc/etext/sac002.htm).