When the Calvinists could not agree with the established religious doctrine, they both broke with the Roman Catholic Church, which resulted in the Religious Wars of the 16th century, and with the Lutherans, differing from their fellow Protestants on the doctrines of Communion and other theories of worship.
A. which resulted in the Religious Wars of the 16th century, and with the Lutherans, differing -- which refers to the church, i.e, church resulted in the religious wars of the 16th century. This is non-sensical. ELIMINATED
B. resulting in the Religious Wars of the 16th century, and the Lutherans, who differed -- "and the Lutherans, who differed", makes the second part of the sentence a run on statement. It doesn't link with first part. ELIMINATED
C. which resulted in the Religious Wars of the 16th century, and abandoned the Lutherans, who differed -- same error as in A. ELIMINATED
D. resulting in the Religious Wars of the 16th century, and abandoned the Lutherans, differing -- CORRECT. It restores the meaning of the sentence.
E. resulting in the Religious Wars of the 16th century, and also abandoned the Lutherans, who differed -- "also" can be used when we have either "not" or "not only" in a sentence. "who" is redundant here. ELIMINATED
OPTION: D