I thought Ron D. Moore said that all of the final five appeared in the last episode and that clues to the identity of the unrevealed Cylon were scattered through the programme? This would diminish your theory but it prompted me to remember that Lampkin's comments suggested Jospeh Adama was a close observer of people and a proficient liar. Another issue that could clinch it isn't the dramatic angle but production realities. Using a core member of the cast would provide surprise and keep costs down.

This got me thinking again. When a reference was made to the one who programmed them, most people would assume that was a Software Engineer but what if the programming refered to wasn't software but moral programming? As a wild speculation might it be possible that the religion and outlook of the Cylons is a direct result of some legal action or intervention by Joseph Adama? It's a further stretch but "Adama is a Cylon" could be meant in a spiritual sense.