We do not know the specifics of Nehor’s self-defense, but Alma’s reaction to the case begins with a denouncement of priestcraft. Notice how odd this seems to our modern sensibilities. We have a man who is guilty of murder, and the most important crime he commits appears to be priestcraft! More than the concern over Nehor as a murderer is the concern over Nehor as a man who preaches priestcraft. Why?
In killing Gideon, Nehor had certainly deprived Zarahemla of a respected man. However, even though that one man is irretrievably lost, he was nevertheless a single man. By preaching priestcraft, however, Nehor was undermining the entire social structure. This was a crime against all of the people of Zarahemla as it would foment dissention and schism. Nehor might not kill again, but he would certainly be a great harm to society as a whole as he created dissentions among the people. It was those types of dissentions that had created the civil war in the time of Benjamin, leading many to leave Zarahemla to join with the Lamanites (see Words of Mormon 1:15-16). In the long view, this was a much more dangerous crime than a murder of a single man in the heat of passion.