In spite of the difficulties, the Lord turns completely away from the idea of destroying the unproductive trees and to the task of saving the essence of all of them. While the process will leave some parts of each type of tree to destruction, yet the Lord will salvage the good from each and bring all back together.
Certainly this aspect of the allegory is clear. God will save all of his children who are capable of salvation, those who will choose to turn back to the Lord. Even though we may, as a general people, have strayed, nevertheless the Lord will continue to strive to save all those he can, and to bring them back to one gospel.