The Greek word musterion, most often translated as "mystery" in the New Testament, had a specific meaning throughout much of the ancient world when Paul wrote his epistles. This word was used by the mystery religions of his day to refer to a secret rite or teaching that was given to those who were initiated. Since musterion generally referred to a religious ritual, the translator(s) of the Latin Vulgate frequently translated the word as sacramentum (Daniel 2:18; 4:6; Tobit 12:7; Ephesians 1:9; 3:3,9; 5:32; 1 Timothy 3:16; Revelation 1:20). Paul clearly employed this term in this way in 1 Corinthians to refer to esoteric rituals the "mature" Christians practiced (1 Corinthians 2:6). These Christians were those who were no longer "babes" in the gospel and who could endure "adult food" and not just "milk" of the gospel (1 Corinthians 3:1-2). In this context, Paul referred to himself as one who dispensed or oversaw the "mysteries" (1 Corinthians 4:1). Paul upbraided the Corinthian saints for not being ready yet to receive these mysteries.
These secret rituals and teachings had their origin in Christ's forty-day teachings according to Clement of Alexandria, and they clearly continued among some circles in the early Church as shown by Justin Martyr, the Clementine Homilies, Clement of Alexandria, Origen, and others. Due to heavy external persecution, all of the sacraments became "mysteries" being performed in secret to avoid the scrutiny of outsiders. Eventually the separate esoteric rituals spoken of by Paul were absorbed into the common rituals of baptism, confirmation, and the Lord's Supper and thus lost their separate identity.
This paper will first investigate the etymology and meaning of the word "mystery" and then demonstrate that these "mysteries" were a part of Pauline-Christianity. From this foundation, the paper will then show the continuance of these esoteric rituals and their absorption into the exoteric rituals resulting in their eventual loss in the early Christian Church. While not expressly tied to the ancient temple, there is considerable evidence that these teachings grew out of temple theology (see Barker, Margaret, The Secret Tradition).
I've read quite a bit on this topic, but for any of you early Church history buffs out there who may know of some interesting sources, any suggestions are welcome.