Here both 𝓟 and the 1830 edition had the plural were in the relative clause. Grammatically, the plural is correct since the delayed subject is semantically plural (“there were so much wickedness and so many murders committed”). In the 1837 edition, the were was changed to was, perhaps unintentionally since the change was not marked by Joseph Smith in 𝓟. The singular was was most likely the result of considering as the subject only the immediately following singular noun phrase, “so much wickedness”. The original text allowed for both was and were with plural subjects; for discussion of this, see under 1 Nephi 4:4 (as well as more generally under subject-verb agreement in volume 3).
Summary: Restore in 3 Nephi 5:6 the original plural were (“in the which there were so much wickedness and so many murders committed”); in this case, the plural form is grammatically correct.