That's pretty interesting. It would also explain how Dr. Shaw's totemic crucifix worked into the symbolism.
My issue wasn't necessarily plot holes as much as how the script seemed to abandon its philosophical nature in the 2nd Act. For example, the remaining Engineer is a being from a race that mastered intergalactic travel 5,000 years before us...and yet his role in the movie is essentially bashing people's brains in like a gorilla.