Schaeffer credits Knox's "theory of the justification of revolution" with planting the seeds that were later nurtured by men like Samuel Rutherford who wrote Lex Rex.  Here's Schaeffer's analysis of Rutherford's thought (emphasis mine):

Rutherford argued that Romans 13 indicates that all power is from God and that government is ordained and instituted by God.  The state, however, is to be administered according to the principles of God's Law.  Acts of the state which contradict God's Law were illegitimate and acts of tyranny.  Tyranny was defined as ruling without the sanction of God. (p. 100)

Then Schaeffer itemizes several of the arguments that Rutherford used to establish the right and duty to resist an "unlawful government" and leads to that chapter's exciting conclusion (emphasis mine):
   

Rutherford offered suggestions concerning illegitimate acts of the state.  A ruler, he wrote, should not be deposed merely because he commits a single breach of the compact he has with the people.  Only when the magistrate acts in such a way that the governing structure of a country is being destroyed - that is, when he is attacking the fundamental structure of society - is he to be relieved of his power and authority.
    That is exactly what we are facing today.  The whole structure of our society is being attacked and destroyed.  It is being given an entirely opposite base which gives exactly the opposite results.  The reversal is much more total and destructive than that which Rutherford or any of the Reformers faced in their day. (p.101-2)

   
These words were not written in the twenty-first century as our country is led by men who launch pre-emptive wars, suspend the constitution, engage in domestic spying, detain people without benefit of trial, violate the Geneva Conventions and justify torturing prisoners.  These words were written in the early 1980's, as Ronald Reagan was beginning his Presidency.

 The next chapter in Schaeffer's book is entitled, "The Use of Civil Disobedience" and in it he discusses the use of force.  He writes (emphasis mine):

When discussing force it is important to keep an axiom in mind:  always before protest or force is used, we must work for reconstruction.  In other words, we should attempt to correct and rebuild society before we advocate tearing it down or disrupting it. (p. 106)

Then Schaeffer goes on to describe a situation in which there may be no other effective protest than civil disobedience (Italics are Schaeffer's):

The problem in relation to a state public school system is not just an abstract possibility.  As I write, a case of undue entanglement and interference is in the courts in a situation that corresponds exactly to Samuel Rutherford's concept of the proper procedure for a corporate body to resist.
    The state of Arkansas has passed a law allowing creation to be taught in the public schools.  The American Civil Liberties Union (ACLU) is trying to have this law revoked, saying it violates the separation of church and state.
    Here is a clear case fitting Rutherford's criteria.  The State of Arkansas has passed a law.  The courts are being used by the ACLU to try to nullify a state law which has the support of the original meaning of the First Amendment.  The ACLU is arguing its case based on a certain concept of the separation of church and state.  But it must be stressed that this concept is entirely new and novel from the viewpoint of the original intent of the First Amendment and the total intent of the Founding Fathers.  This new separation concept is a product of the recent humanist dominance in the United States and is being used in this case to destroy the power of a properly elected state legislature's "sovereign" ruling.
    The ACLU is acting as the arm of the humanist consensus to force its view on the majority of the Arkansas state officials.
    If there was ever a clearer example of the lower "magistrates" being treated with tyranny, it would be hard to find.  And this would be a time, if the appeal courts finally rule tyrannically, for the state government to protest and refuse to submit.  This fits Rutherford's proper procedures exactly. (pp. 109-110)

Schaeffer's next chapter is entitled, "The Use of Force."  It begins with these words,

There does come a time when force, even physical force, is appropriate.  The Christian is not to take the law into his own hands and become a law unto himself.  But when all avenues of flight and protest have closed, force in the defensive posture is appropriate. (p.  117)

Schaeffer goes on to encourage Christians to get involved politically and exercise political force.  He contends that he is "in no way talking about any kind of theocracy." (p. 120)  He adds,

We must not confuse the kingdom of God with our country.  To say it another way:  "We should not wrap Christianity in our national flag."
    None of this, however, changes the fact that the United States was founded upon a Christian consensus, nor that we today should bring Judeo-Christian principles into play in regard to government.  But that is very different from a theocracy in name or in fact.  (p. 121)

Schaeffer is not fully in the Christian Reconstructionist camp.  Neither does he seem to be a "Christian Nationalist."  Rather, he appears to be advocating the establishment of a majoritarian religion in each state.   Doing so, however, requires "strict constructionist", "state's rights" interpretations of the Constitution that ignore the influence of the 14th amendment on our jurisprudence since the civil war.