According to the Midrash, the Jews killed the enemies inside their houses with the sword, but killed those who were outside with other methods. Those who were hiding needed to be brought out to the battlefield.
The Alshich explains that some gentiles openly threatened the Jews, while others harbored hate privately. Each group received a punishment commensurate with their behavior – some were wounded with the sword, some were killed, and yet others were destroyed together with their possessions.
The Maharal points out that hitting the enemies with the sword could potentially kill them, and once they are killed, they may need to be buried. But once they are destroyed, the enemies are gone.
R’ Moshe Katzenellenbogen writes that, in big cities, Jews could only kill bigger, more obvious enemies. In the smaller cities, the Jews stripped the weaker leaders of their power and humiliated them.
The Vilna Gaon explains these three methods were utilized at different stages of the battle. During the first stage, the Jews used swords, then graduated to burning those hiding out of the buildings, and finally arrested the residents.
The Ben Ish Chai points out that the rearranged initial letters (not counting the article letter vuv‘s) of makas cherev vi’hereg vi’avdal (“striking of the sword, and killed, and destroyed”) spell out the word emcheh (“I will destroy”). H-Shem (Shemos 17:14) uses this very word in His promise to eradicate Amalek, the nation responsible for this massacre. He also points out that these three expressions parallel Haman’s plan (Esther 3:13) to kill, destroy, and annihilate the Jews. The Jews merited to overcome this triple fate by fasting for three days (Esther 4:16).
R’ Dovid Feinstein writes that the destruction in this verse refers to the Jews destroyed the property of their enemies. This was done to demonstrate that their intent was not to conquer the wealth of others. Perhaps this was also intentionally contrary to Achasverosh’s order (Esther 4:11) in order to have the excuse that they could not take the possessions, since they were destroyed.