The solution for the main tree is to take drastic measures. The important statement is that the roots are good. Those roots are the covenants God has made with the house of Israel. Those covenants are good and remain for those who can access them. The Lord of the vineyard does not see a reason to alter the covenants themselves.
The blame is put on the wild branches, which have been identified as the gentiles. Thus, this part of the allegory would describe the time of Christian apostasy. It was a time when there was a great increase in the numbers of Christians, but the loss of some of the pure doctrines had made it difficult to receive the full benefits of the covenant with the house of Israel.
Once again, a possible solution is to destroy the entire experiment, but that is not what the Lord of the vineyard desires. The desire is to preserve the roots, or the covenant, if at all possible.