Is there a time when God permits anger?

Does the Bible provide examples to the above question? Yes. There are many examples of what is called righteous indignation. We should be angry about what the Lord is angry about. Unfortunately, we are often laughing and making light of what God hates. We can attribute that to our fallen sinful nature.

We are so desensitized to sin that things that are heinous in the sight of God are pleasurable to us. 
Jesus said in John 3:19b, "Men loved darkness rather than light because their deeds were (and are) evil".

Yes, this is one of those articles that will step on toes, mine included. And by me writing this article, it makes me even more culpable for my actions - something the natural man hates to admit. 

Phineas

Phineas was a priest during the time of Moses. He was the son of Eleazar who was the son of Aaron, the first High Priest of Israel. Aaron and Moses were brothers.  Aaron was dead by this time and his son Eleazar was installed as High Priest after him (Num 20:28-29). 

In Numbers 25 we read of Israel committing gross sin. They are intermarrying with the Moabites, sacrificing and worshiping their gods - idolatry. This violates the first two commandments inExodus 20:2-6).  This angers the Lord so He commands Moses to kill all the perpetrators. Phineas sees a Hebrew man bring a foreign woman to his tent so he grabs a spear and kills them both, through the man's back, and through the woman's stomach. 
  
Why would Phineas commit this seemingly gross act of murder? We discover as a result of Israel's sin, God sent a plague of death through the land. Phineas was angry for the Lord's sake. Killing the Hebrew man and woman was an act of righteousness that ended the plague, not before it claimed the lives of 24,000 people (Num 25:9). God commended Phineas for this and promised him a covenant of peace (Num 25:12).

Samuel 


The Amalekites were enemies of Israel for around 350 years during the time of the Prophet Samuel. The Lord promised that He would blot out the name of Amalek from under heaven during the time of the Exodus (Ex 17:14-15). A short history of the Amalekites: Amalek was the grandson of Esau the twin brother of Jacob (Gen 36:12). God commanded Samuel to give word to King Saul to destroy the Amalekites. Saul did not obey the Lord's command. He saved the best animals. He also spared their king, a man by the name of Agag. Samuel obeyed the word of the Lord and hacked Agag in pieces (I Samuel 15:33). 

Again, this was Samuel executing divine judgment on behalf of the Lord's wrath. It had to be done. This occasion was the perfect time to be angry because it was divine justice. Agag was an evil man and was doomed to destruction. Samuel being a righteous man was grieved by Saul's disobedience. The disobedience led to Saul's throne being taken away and given to David (I Sam 15:28).

The Corinthians 

In I Corinthians 5 we read of a man having a sexual relationship with his father's wife - his step mother. This sin was so gross that Paul said that the heathen would not engage in it (vs. 1). What made this even worse was that it was happening among professing Christians! Paul was outraged, but the Corinthian church was not. Rather they were arrogant. What should have happened is that the sinning member should have been removed from their assembly until he repented. Since it was not done there, Paul tells them to "put out that wicked person" (vs. 13).

There should have been grief over his sin instead of apathy among the congregation. It is important to remove the evil person before their ways influence others to commit sin as well. If allowed to remain in the bosom of the church the person believes there is no divine retribution for their sinful behavior and others will follow their evil ways deceiving themselves into thinking one can live anyway they want and God not chasten them for it (Heb 12:5-11).

Paul said later in this same letter that, "Do not be deceived, bad company corrupts good morals" (I Cor 15:33).

What do these accounts teach us? There is a time to be angry - when God is angry. In each instance God commanded his servants to take action. To ignore the righteous anger of God is sin, and will be met with retribution on those who ignore His divine command to execute justice.

Please understand the last account is in regard to the Church, the people of God. God judges the outside world (I Cor 5:12).

Here is the balance we must have, "Be angry and do not sin; do not let the son go down on your anger, and do not give the devil an opportunity" (Eph:26-27).

We are commanded  to be angry against evil for it will manifest the righteousness of God and show the sinner their sin clearly. This can drive them to godly repentance and ultimately salvation.

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