DISCLAIMER: I’m not Catholic, so I apologize for any mistakes related to that.
--SHORT ANSWER--
Richard is a Catholic who – in order to atone for murdering the doctor (at the beginning of Ab "Aeterno") – modeled The Others after the Catholic Church, the official language of which is Latin.
--EVIDENCE--
Based on his conversations with Jacob in Ab Aeterno, we can assume that Jacob recruited Richard as his sole intermediary to let people who arrive on the Island know what Jacob wants them to do without Jacob actually having to interfere in people’s lives. Richard likely founded The Others in order to help him do this (exert Jacob’s influence on those that arrive on the Island).
Richard is obviously a Christian and almost definitely a CATHOLIC (given that he was a Spaniard in the 1800s). In addition, since Jacob convinced Richard the MIB was trying to trick him (when MIB told Richard that Jacob was the Devil), Richard probably saw MIB as the Devil and Jacob as God. (Note: I’m NOT trying to say that Jacob actually is god, just that Richard thought Jacob was when Richard started The Others.)
Being given a mission from god made Richard see himself as a priest. Therefore, he would want to follow (and have The Others follow) the principles of the Catholic priesthood as much as possible. One of these principles is speaking in Latin.
***Other “Other” ties to Catholicism: There is a picture of Brother Campbell, (the monk who helped Desmond in the Episode Catch-22) on Eloise Hawking’s desk. Richard’s role as the voice of Jacob on the Island is similar to that of St. Peter, who was the first pope. And, like St. Peter, there were other popes/leaders after Richard. Also, the Season 6 promo photo was modeled after The Last Supper. Finally, Richard was “baptized” in the ocean by Jacob when Richard was trying to kill him.