As discussed under 2 Nephi 22:2, the original Book of Mormon text had a few cases where the perfect auxiliary for the verb become was the archaic be rather than the modern have. Here in 3 Nephi 7:7, in his editing for the 1837 edition, Joseph Smith changed the perfect were to had. The critical text will restore the original were, giving “although they were nearly all become wicked”. For examples of this usage in the King James Bible, see under Helaman 13:36.
Summary: Restore the original were in 3 Nephi 7:7, an example of archaic English where the perfect auxiliary for the verb become was be rather than have.