If it had already been obvious that Nephi was viewing Isaiah in relation to his vision of the future, this discussion of the great and abominable church could not be more obvious. In the Book of Mormon, Jacob is the only other writer to use the phrase, and Jacob refers to it in his discussion of the verses from Isaiah 49 that Nephi assigned him. What Jacob teaches appears close enough to Nephi’s exegesis here, that it is a reasonable assumption that Jacob learned it from Nephi.
In this exegesis, the great and abominable church is contextually defined as “every nation which shall war against” the house Israel. Thus, as the Lord shows his power in the last days, the great final battle between good and evil is represented by Israel and the great and abominable church. In the end, Jehovah, and therefore Israel, will be triumphant.
The theme of Satan having no power over the hearts of the children of men and the burning of the wicked clearly place this part of the prophecy in the last days, further highlighting the symbolic nature of the great and abominable church.