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So, "pontifex maximus" means "highest pontifex." The Pontifex were, at one time, the priests of the Imperial cult, but over time the meaning of the word broadened and it was used as a word for, "Bishop." The Pope's (unofficial) title is used in that context.
Refusal to use the term (where it clearly applies) would be akin to refusing to use the word, "Tuesday" because it is etymologically linked to the Norse god TΓ½r.