In filmmaking, when something is ‘on the nose’ it means it’s conveying the idea way too directly and obviously. It’s most commonly used to refer to badly written dialogue in which a character says exactly what he or she is thinking.
'On the nose' writing allows for no depth, because depth is created by the contrast between what's said and what's thought (or felt). This applies whether we're talking about character dialogue or whole scenes.
So when Ridley Scott refers to the explicit inclusion of Space Jesus as 'too on the nose', what he's saying is that actually stating it outright would have been too unambiguous. It does not mean that the idea has been discarded altogether, just that he opted for greater subtlety in conveying it. (Feel free to disagree, of course. I am not the Space Pope.)
By the way, I totally missed that David washes Weyland's feet at one point of the movie. And that Janek sacrifices his life with two other guys on either side of him, slightly lower down. Thanks to those of you who pointed that out. I can't THINK what it reminds me of.
Anyway. Like many of you, I had issues with the script. The moment in Prometheus that had me muttering 'oh, for God's sake' in the cinema was during the scene where the crew are scanning the Engineer head. It went like this (and pardon me if I haven't got it exactly right, I'm reconstructing from memory):
Computer screen reads: SCAN COMPLETE. NO CONTAMINANT DETECTED.
Ford: 'Scan complete. No contaminant detected.'
No inflection. No additional value whatsoever. She simply repeats what's on the screen.
That is not just 'on the nose' dialogue. That's 'embedded in the sinal cavity' dialogue.
But it's okay! We can just put on our Pretentious Film Critic hats and read this as a tribute to Sigourney Weaver's character, Gwen DeMarco, in Galaxy Quest!
Voice of Computer: Negative, there is no replacement Beryllium Sphere on board.
Gwen DeMarco: [to crew] No, there is no replacement Beryllium Sphere on board.
Tommy Webber: You know, that is really getting annoying!
Gwen DeMarco: [shouts] Look! I have one job on this lousy ship, it's *stupid*, but I'm gonna do it! Okay?
The Prometheus blogging continues here. It never ends, I tell you.