It was at Ephesus that the christian church declared Mary to be the "the God-bearer" in 431 C.E. This move was intended to legitimize christianity in the eyes of the people of Asia Miinor. Prior to 431 C.E. Mary was not recognized by the Christian church.
Many of the Great Goddess's titles were taken, and declared to be the titles of Mary, including; "Queen of Heaven", "Divine Virgin", "Mother of All". Ephesus was chosen for Mary's installation to add legitimacy to the church's claim that Mary, not Diana, was "the Mother of God", the "Mother of All."
The Christians of the time treated Diana with great disrespect. The Council of Ephesus gave Mary the title of theotokos in opposition to the lesser title that Nestorius and much of the Syrian Church preferred: Christotokos. All of the parties involved in the council would have horrified by any confusion of Mary with a pagan goddess.