Pinchas is known as a KANA’I, a zealot. The Bnei Israel had a moral breakdown and were sinning before an idol on their journey from Egypt. A plague broke out among them. Pinchas saw a prince of one of the tribes openly sinning with a Midianite woman. This was an immorality perpetrated against Hashem. Without getting permission, because of his zeal, he killed them both. The Torah then testifies that the plague stopped.
In the opening verses of this Portion Hashem tells Moshe that He was rewarding Pinchas for his act. For by it: HESHIV ET CHAMATI ME’AL BENEY ISRAEL, “…he turned away My wrath from the Children of Israel.” (Num.25,11)
Pinchas had done two things. He took vengeance to protect Hashem’s name and his action was also responsible for stopping the plague. When Hashem explained the reason for the reward He refers only for stopping the plague. Why?
The answer could lie in the fact that Pinchas acted as a zealot. He took extreme steps without authorization. There is even an opinion in the Talmud that they wanted to excommunicate him for this act. This is not permitted even though he did it to protect Hashem’s name.
He was rewarded, however, by Hashem for saving the Israelites from the plague. To save Jews even a zealot act is permitted.