The whole story of Pinchas is filled with question and gore. How is it that we laud a person for killing, even if justified? The Torah seems to make a point of Pinchas by singling him out to receive a special Blessing. What happened with Moshe when he killed the Egyptian beating the poor slave? Exile, brushes with death and no acknowledgement. When Moshe confronted Og or Sichon he isn't praised. Why is this act of Pinchas any better than Moshe's act of self-sacrifice?

The Torah calls Pinchas the son of Elazar, the son of Aharon-Aaron. Now we knew this before,so why is it necessary to state the obvious?

The Kaballah tells us that Pinchas inherited the nefesh-soul of his uncles Nadav and Avihu, who in turn had inherited the Nefesh of Adam, as well as the Nefesh of Kayin- Cain. This is also the soul of EliJah the Prophet. For this reason the Rabbis say, that Pinchas is Elijah!
Now this didn't happen automatically. For a person is born with a unique Soul, different from those who preceded him. Therefore Pinchas was born with a different Nefesh . In fact he is identified as having the same Nefesh as his grandfather Aharon. Aharon's nature was to be gentle and to negotiate with others, with the assumption that people are reasonable. Aharon as was Pinchas, was a man of peace. When Pinchas tried to stop Zimri by his words , he was confronted with the dilemma of dealing with a crisis of great magnitude and with a nature that wasn't working. Try as he may, the Tribes belittled his entreaties to refrain from public immorality which led to idolatry.
In his realization of the impossibility of his standard way to work and seeing that action had to be taken immediately,or else more tens of thousands would die,Pinchas acted.
When a person does a Mitzva the same way that a Tzaddik did before him, then the Tzaddik literally engarbs himself the Soul of the doer of the Mitzvah. Pinchas was now doing Mitzvos in the way Nadav and Avihu did Mitzvos. As they were his inspiration, they entered his body to assist him in the process. When he killed Zimri the souls of the side of Gevurah were attached to Pinchas' soul. At this point Pinchas corrected the defect, if we could say this, of his grandfather Aharon!
For we are left scratching our heads, as to why Moshe hit the rock and Aharon is punished?!
The answer lies in G-D's expectations of us. G-D wanted Moshe to speak to everyone. Moshe was a man of action. If there was injustice Moshe fixed it. If there was an evil ruler, Moshe would destroy him and his army. If there was a scoffer he had to be dealt with severely. This approach is not the Torah approach, for Derochehu Darchey Noam-Her ways are pleasant.Moshe who had a tendency for Gevurah had to learn to deal kindly with people and Aharon who was the epitome of sweetness had to be tough.When Moshe hit the rock he was reverting back to the old Moshe . Aharon who saw Moshe get angrier and angrier as the scoffers taunted him,should have stepped in and reprimanded them . In this way he would have stopped Moshe from expressing his impatience and anger. For Aharon could never be as tough as Moshe. In the process both Moshe and the people would be spared for their errors. For Moshe was told that his primary method had to be with love and kindness. The people on the other hand were out of line. Miriam their sister had just died and they denied Moshe even a few moments to mourn her!
Thus when there was no choice but to be tough , Aharon reverted back to gentleness and understanding, ineffective with scoffers. This was why he was held back in the desert. For in the future, the people would need a firm but gentle hand. The toughness of Moshe was too much and the gentleness of Aharon was ineffective.
Therefore when Pinchas embraced toughness, he was correcting the weakness of his grandfather's love and kindness!
Since he went against his very nature in his attack on Zimri, this is praiseworthy. a man with Moshe's temperament can't be praised for that which is natural. Moshe is glorified for his prayers for Compassion , for his love of Israel. Pinchas was praised for having done what was abhorrent to him in order to save everyone else!