This destruction, this condemnation, will not happen because of God’s intent, but rather because of that which the people choose. Their agency will still work, with terrible results. Those who “perisheth, perisheth unto [themselves].” By this Samuel indicates that they have elected to perish. It is their choices that have led to this result.
Even with this dire prediction, Samuel holds out hope. They are still free to choose, they are still “permitted to act for yourselves.” They can still repent. If they choose to repent, they may still be saved through the Atonement of the Messiah who is coming. If they do not, they perish, “unto themselves.”