This parsha start by lauding Pinchas for his courageous act of kanous - zealousness. Bnai Yisroel are saved because of his act and he himself is granted eternal priesthood and an eternal covenant with Hashem. This would definitely indicate that what he had done was most worthy.
Yet when we take a closer look at the associated halachos, we are perplexed. For instance, the halachah is that if a kanoi first asks beis din what to do, he is never granted permission to act as Pinchas did (Rambam Hilchos Isurei Biah, 12:4). Additionally, the kanoi can only kill the transgressors while they are engaged in the sinful act. If he does so a moment later, he is judged as a murderer and punished. Even more vexing is the ruling (Sanhedrin 81b) that had Zimri turned around and killed Pinchas in self-defense, he would have been within in his rights, and therefore innocent of murder! This all leaves us to wonder: was Pinchas's act laudatory or murder; was Pinchas right or wrong?
The Talmud Yerushalmi (Sanhedrin 48b) goes a step further and states that this type of action is and was diapproved by the Chachomim, and they actually wished to put him into cherem. The only reason they did not do so was because the Divine Spirit declared that a covenant was being forged with Pinchas on account of this act! But how does this square with the dictum, "lo baShomayim he", that the chachomim, and not new information emanating from Heaven, have the final say in determining the halacha? And if, on the other hand, the Divine Spirit does have the final say, then why do the chachomim still disapprove of kanoim?
The topic of kanous also raises troubling questions about a society that allows itself to be run by extra-judicial actions and vigilantes. Is this not anarchy?
The Akeidah (Sha'ar 83) give us tremendous insight into this parsha and I will try to rephrase his lengthy and somewhat hidden words.
The world of miztvos is aimed at one's rational faculties. The mitzvos of punishing sinners comprise a mandate imposed on the courts of Klal Yisroel. Concomitantly, those sins that are beyond the pale of human judgement, are only for G-d to judge and punish as He sees fit.
A person, however, possesses a spirit, that rises above his intellect. If a man is so moved by righteousness that he abandons logic and is willing to sacrifice himself [e.g. Pinchas exposing himself to the possibility of Zimri killing him in self-defense], it is his spirit rising to the occaision. His soul, thereby becomes an emissary for the Divine Beis Din, so to speak, and he is now acting as an agent of the Divine Court, not as an agent of a human beis din.
An analogous situation would be where one sees an innocent person being murdered. Assuming the witness has no chance of rescuing the victim, reason dictates that he protect his own life by not intervening. But if this witness has such a strong sense of moral outrage that he nonetheless stands up and fights the attacker - even if it was to no avail, and makes "no sense" - we would commend his noble spirit of righteousness, that could not sit idly by and tolerate the injustice that was being perpetrated. Thus kanous is not, and can't be, mandated. It must be the spontaneous reaction of a noble spirit who can't tolerate evil, no matter what the consequences.
Rav Moshe Chaim Luzzato (Mesilas Yesharim, chapter 19) phrases it thus:
It is obvious that a person who truly loves his friend will not be able to tolerate someone hitting him or humiliating him, and will surely defend him. Similarly, one who loves Hashem's Name will not be able to see its desecration by a wanton disregard for transgressions.
This kanous is, on the one hand, an expression of the ultimate nobility of the human spirit. But on the other hand, it is greatly suspect. It requires an extraordinary purity of motive and precision of timing.
The Netziv (Ha'amek Davar, Breishis 34:25) expresses this most precisely when describing Shimon and Levi's killing of Shechem:
Though the two brothers were united in their great fury, and personal endangerment, their motives were extremely different. One was merely expressing the human response to an insult to family pride, and that is an "alien fire" [i.e. an improper and un-Jewish motive.] The other was coming with a zealousness for G-d's justice without personal interest or gain. But even that motive needs to be applied at the right time and place, for if not, it too can be very destructive.
Yes, the rabbis condemn zealousness, for it is a non-halachic response, done out of motives that are suspect. But when the Divine Spirit revealed to us that Pinchas was the unique individual whose actions stemmed from the noblest of spirits and purest of motives, expressed at the right time and place, then we rightfully hail him as the savior of Israel!