It is important to make the difference. From Nimrod to Pharaoh; going through Haman, Antiochus Epiphanes and Nero; continuing with the Catholic Inquisition, the Protestant Peasants' War in Germany, the European murderous conflicts between Catholics and Protestants; all the way to Western enslavement of the blacks, Hitler, Bosnia, Sudan, and today's insane extremists, History is filled with the murders of people who justified heinous murder by covering it with a cloak of religiosity so-called!
Many people use the story of Pinchas as justification for their bigoted hatred. The command for The Children of Israel to kill the people of Cana'an in order to conquer the land Hashem had given them has also been used in that way.
The stories in the Torah have to be read in wisdom, balancing one with the other. If we don't, we will believe that like Abraham it is honorable to sacrifice our child for God, or do like Jephta who offered his daughter as a thanksgiving to God for winning the war. Not reading these things in wisdom makes people believe today that polygamy and slavery are Biblical institutions. The stories in the Bible are not meant to teach us one-size-fits-all doctrines. They are meant to teach us principles, and we can use these principles to lead our lives today. Reading their with wisdom is to find these golden principles.
Reading with wisdom also means to compare stories and balancing scripture with scripture. Abraham knew the difference. When he arrived in Cana'an from Ur, the patriarch saw that the Land was already occupied. Though he had a divine oracle for Its possession, Abraham did not go forcefully to conquer but went to Egypt Instead aand came back at a more opportune time. Later, when the five kings came, he did not go by yesterday's information. He set out to war against them. His cues came from the direct command of God at the time and place of action. In each situation, Abraham reset the equation so to speak and tried to find out what it is that he was supposed to do at the time.
As believers, where do our cues come from? From Pinchas? Joshua? The words of King David? Jeremiah? Mattatias Maccabeus? We can find anything in the text of the Tanach in order to justify our actions. There are times when the Children of Israel were told to go to war and defend themselves and annihilate whole civilizations. At other times, they were told to send their worship leaders to battle. And yet, in other situations, they were told to either stay put and not do anything or even to surrender to the enemy. How do we know what to do? Where do our cues come from? From our Commander-in Chief!
As believers, our Commander-in Chief is Yeshua. He is the Captain of the Armies of God. His emissaries to us are Yochanan, Shaul, Ya'akov, and Keifa of whom we still have letters of instructions, and who all promoted the teaching of their and our commander in Chief: Yeshua; Yeshua of whom we still have many words of direction and instruction. To know how to act in these situation concerning the End of Days which started at the advent of the birth, death, and resurrection of our Master until today, we must study the acts and teachings of the Master as well as those of His disciples. Our days and the battles we face are very similar to theirs so their words apply to us. Their words were words of prophecy that concern their times, and ours.
The Brit haHadasha gives us plenty of information to base ourselves from, but also Fox's Book of Martyrs, Ecclesiastical History (Eusebius), The Josephus volumes, as well as The Didache have much to offer in order to learn how the disciples handled living in a world much like ours today. This is where we take our cues from.
Pinchas may have deferred Hashem's anger from Israel, but the zealotry of the Days of the Master blinded the eyes of many to the Mashiach that had come to them. It also caused Jerusalem and the Temple to be destroyed in 70 AD, and Israel to vanish from History for 2000 years in the second revolt. The difference might be in the attitude. Pinchas' was one of true love for the people of Israel, while the zealots was of anger and wrath against idolaters and their enemies. It is the difference between a man and a cat. Both want to get rid of the mouse. One is to protect the house and he is satisfied once the mouse is gone while the other is for the joy and thrill of killing as the cat will not be satisfied; he will desire to kill another mouse.
You can probably find the Brit's passages of instruction on how to deal with our world today yourself, but I will end with this one statement from Ya'akov, the Master's own brother and leader of the Israeli congregations after Yeshua's departure:
A person's anger does not accomplish God's righteousness!
(Jas 1:20 CJB)