Here are some Rutherford quotes, but a few points first. The natural law tradition has always maintained self-defense as a normal given. The enormous burden of proof is on the negative. As pertaining to the Exodus case law: if it is summative of the moral law, being a practical example of maintaining human life (6th commandment, plus one's family) and maintaining just wealth (8th Commandment), then its binding today. The only difficulty is in applying it in some of the statist parts of America.
If we deny that one can use this law, then we are back to the natural law question. If we reject natural law, then the choices are theonomy are Anabaptist chaos.
And shall it excuse the estates, to say, we could not judge the cause of the poor, nor crush the priests of Baal, and the idolatrous mass-prelates, because the king forbade us? So might the king break up the meeting of the lords of session, when they were to decern that Naboth’s vineyard should be restored to him, and hinder the states to repress tyranny; and this were as much as if the states should say, We made this man our king, and with our good-will we agree he shall be a tyrant. For if God gave it to him as a king, we are to consent that he enjoy it. (97)
But the conclusion is absurd, and denied by royalists. I prove the connection: If the king have such a power above all restraint, the power itself, to wit, king David’s power to kill innocent Uriah, and deflower Bathsheba, without the accident of being restrained or punished by men, it is either from God or not from God. If it be from God, it must be a power against the sixth and seventh commandments, which God gave to David, and not to any subject; and so David lied when he confessed this sin, and this sin cannot be pardoned because it was no sin: and kings, because kings, are under no tie of duties of mercy, and truth, and justice to their subjects, contrary to that which God’s law requireth of all judges (Deut. i. 15-17; xvii. 15-20; 2 Chron. xix. 6, 7; Rom. xiii. 3, 4): (103)
Whatever David did, though he was a king, he did it not as king; he deflowered not Bathsheba as king, and Bathsheba might with bodily resistance and violence lawfully have resisted king David, though kingly power remained in aim, while he should thus attempt to commit adultery; else David might have said to Bathsheba, “Because I am the Lord’s anointed, it is rebellion in thee, a subject, to oppose any bodily violence to my act of forcing of thee; it is unlawful to thee to cry for help, for if any shall offer violently to rescue thee from me, he resisteth the ordinance of God.” Subjection is due to Nero as an emperor, but not any subjection is due to him in the burning of Rome, and torturing of Christians, except you say that Nero’s power abused in these acts of cruelty was, 1. A power from God. 2. An ordidance of God. 3. That in these he was the minister of God for the good of the commonwealth. (149).
Rutherford notes on p. 153 that on the Statist gloss, and in accordance with what Charles I wanted to do (e.g., hiring Irish Catholics to come and kill English Protestants), the English Protestants were obliged to lay down arms and let the Irish Catholics kill them.
In the greatest sentence in Lex, Rex, Rutherford says we should rather unhorse the Irish Catholic and throw him off the bridge.