How is the "spirituality of the church" consistent with theonomy? In Hart and Muether's history of American Presbyterianism, Seeking a Better Country, they describe a doctrine of the "spirituality of the church," which emphasizes the spiritual, not social, task of the church:


  The church was not commissioned to make the world a better place in which to live.  It had no business telling the government how to rule the body politic.  It was not to feed the hungry, or provide houses for the homeless, or protest social injustice.  These political and social temptations only distracted the church from its spiritual calling. (223)


This view was "championed by James H. Thornwell," one of the most prominent 19th-century Southern Presbyterians.  But in what seems to me a contradiction, Thornwell is cited by others as an advocate of theonomy, which Wikipedia defines:


  the idea that God's Law-Word, including the judicial laws of the Old Testament, should be observed by modern societies.


For example, theonomist Greg Bahnsen writes:


  Even into the late nineteenth century respected Reformed theologians were contending that the state should conform its laws to those found in the law of God. The southern presbyterian, James H. Thornwell, stated in 1861: "We long to see, what the world has never yet beheld, a truly Christian Republic." (source)


Put simply, my question is: how are these two views are reconciled in the thought of Thornwell and other theologians who hold these two views?  How did he/they see the spirituality of the church and theonomy as non-contradictory?
Theonomy recognizes that the revealed word of God is the rule in every area of life, not merely the spiritual matters. Theonomists interpret the Bible to prescribe civil laws, especially from the Israelite theocracy that are supposed to govern all civil governments that are in line with God's will. They recognize both the civil magistrate and the Church as legitimate institutions who owe their allegiance to the word of God but they are not the same institution. In their view, it would be inappropriate for either institution to interfere with the matters that concern the other. Church courts are never to exercise civil penalties over their judgments nor are civil courts to usurp the ministry of the keys or the sacraments from the Church.

This view is not unique to James Thornwell, but it is clearly evident in his thinking.


  [T]he separation of Church and State is a very different thing from
  the separation of religion and the State. Here is where our fathers
  erred. In their anxiety to guard against the evils of a religious
  establishment, and to preserve the provinces of Church and State
  separate and distinct, they virtually expelled Jehovah from the
  government of the country, and left the State an irresponsible
  corporation, or responsible only to the immediate corporators. They
  made it a moral person, and yet not accountable to the Source of all
  law. It is this anomaly which we desire to see removed; and the
  removal of it by no means implies a single element of what is involved
  in a national Church.



James H. Thornwell's Critique of the Confederate Constitution