JOEL - I see no conflict here. Both versions of this scripture are doctrinally correct. Jesus is the God of this earth and universe, therefore the virgin Mary is the mother of God in the flesh. But since Father in Heaven is also a God, this simple change was made to clarify which God the Book of Mormon is talking about in this scripture. There are a few other similar scriptures like this that were changed so we know for sure which God they were talking about(1 Nephi 13:40, 1 Nephi 11:21, 1 Nephi 11:32).
For example, the 1830 edition of 1 Nephi 11:21 said:
"And the angel said unto me: Behold the Lamb of God, yea, even the Eternal Father! Knowest thou the meaning of the tree which thy father saw?"
The way the sentence is structured here it sounds like he is calling Jesus the Eternal Father, although as a member of the godhead Christ can bear the title of "Eternal Father". But the "Eternal Father" title in this case is refering to the word "God" in the previous phrase and not to the word "Lamb". To avoid confusion it was changed it to read, "even the Son of the Eternal Father".
Joseph Smith himself made these changes in the 1837 edition of the Book of Mormon. Many critics claim these changes were made because Joseph was changing his mind about the nature of the Godhead. But there are other scriptures in the Book of Mormon that were not changed that demonstrate that he always believed them to be two separate individuals (2 Nephi 25, 2 Nephi 31)
Neither Joseph Smith nor the LDS church have ever believed that there was one single God in heaven who was born to Mary as Jesus Christ. If Joseph Smith believed this and wrote the Book of Mormon himself, as many critics claim, why then would he have Jesus praying to the Father(3 Nephi 19:24)? Joseph made the changes to accommodate those who might be reading it for the first time, who do not have a true understanding about the nature of the Godhead and so they would not confuse it with how the other Christian faiths perceived God.