The destruction will be of the Nephites, but their enemies will remain. The Lord’s anger is visited upon the people who should have known better, not those who had never accepted the gospel. This principle that relates the severity of the punishment to the opportunity to do better was taught by the Savior himself during his ministry:
Luke 12:47-48
47 And that servant, which knew his lord’s will, and prepared not himself, neither did according to his will, shall be beaten with many stripes.
48 But he that knew not, and did commit things worthy of stripes, shall be beaten with few stripes. For unto whomsoever much is given, of him shall be much required: and to whom men have committed much, of him they will ask the more.
The Nephites will become the collective examples of the Savior’s parable of the servants.