As with the triumphal entry prophesied in Isaiah, the Messiah will be in their midst and will usher in a time of peace. It must have been very painful to Nephi to speak of the peace of the Lord, and in the same sentence have to limit its duration on the earth.
To be certain, Nephi understood the difference between this coming of the Messiah and the final apocalypse. In 2 Nephi 30:8-12 he is very clear that he sees the final days:
2 Ne. 30:8
8 And it shall come to pass that the Lord God shall commence his work among all nations, kindreds, tongues, and people, to bring about the restoration of his people upon the earth.
2 Ne. 30:9
9 And with righteousness shall the Lord God judge the poor, and reprove with equity for the meek of the earth. And he shall smite the earth with the rod of his mouth; and with the breath of his lips shall he slay the wicked.
2 Ne. 30:10
10 For the time speedily cometh that the Lord God shall cause a great division among the people, and the wicked will he destroy; and he will spare his people, yea, even if it so be that he must destroy the wicked by fire.
2 Ne. 30:11
11 And righteousness shall be the girdle of his loins, and faithfulness the girdle of his reins.
2 Ne. 30:12
12 And then shall the wolf dwell with the lamb; and the leopard shall lie down with the kid, and the calf, and the young lion, and the fatling, together; and a little child shall lead them.
In these verses, Nephi describes the final coming, and includes both a burning and a righteous remnant that is spared (and also cites Isaiah). The point is not that Nephi confused the coming of the Messiah to the New World with the events of the end of time, but that he sees them in the same terms, and as parallels in the spiritual history of the world.