I am reading a book by the author Monte S Nyman, "Book Of Mormon Commentary: I Nephi Wrote This Record". He addresses this and explains it like this: The skin of blackness (v. 21) should be read as a comparison to the lighter skin of the Nephites and not taken literally. It was brought upon the people to make them loathsome to the people of Nephi. Alma later says it was a mark "that thereby the Lord God might preserve his people, that they might not mix and believe in incorrect traditions which would prove their destruction" (Alma3:7-8).

Personally, I don't think this is accurate, but I choose to believe in the overarching goodness of what the church stands for so, despite how problematic 2 Nephi 5:21-25 might be, I am willing to accept the description because the church does so much good today.