After the unification of the House of Israel, including the adoption of the Gentiles who are “no more confounded” (as Nephi recorded in verse 2), the great and abominable church itself—the cause of confounding the Gentiles—will be brought down.
The great pit is that gulf that Nephi saw between the world and the narrow path. It will be filled in. The image of the gulf symbolized the difficulty of those who entered the spacious building from returning to the narrow path. With that gulf filled in, there will be no great obstacle to repentance.
This is the reason that verses 5 and 6 speak of the Gentiles repenting. In some ways, the Gentiles had been representatives of the great and spacious building, but they can, and must, leave it. They must cross the gulf. They must walk the narrow path, else they must perish. The great and abominable church has not been destroyed at this point in the vision, and it remains a possible destination.