Missionary Romanization?
Confucius is a latin transliteration as opposed to an English one. Etymology might be a good starting point: http://www.etymonline.com/index.php?term=Confucius

This article is probably highly relevant: http://en.wikipedia.org/wiki/Jesuit_China_missions

Further reading: http://www.amazon.com/WINDOWS-INTO-CHINA-JESUITS-1580-1730/dp/B000ID3EIE