Granted all of the above, but again I keep reading things you take as CATEGORICALLY being religious references without being convinced they couldn't mean anything else. That's the whole point of interpretation. Not one example you have given does anything to reassure me that this is anything other than your own personal take. (I'm going by the quality of your posts as an indication you are beyond reciting received wisdom so to speak).
Ilia mentions her oath of celibacy, could be a virginal reference as you say, could be a framing for the theme of exploring one's emotional development - a far more commonplace theme within trek. It could simply be there to build up emotional depth for the Decker/Ilia relationship.
The holy triumvirate you speak of, Spock, Kirk, McCoy. It's easy to read meaning into that within the context of the film but that doesn't take into account the fact that they were inherited from three season's character development and NOT using the established relationships between them would have jarred with fans to say the least.
The same sort of case could be made about any of the things you mention. Just because they could be taken as reflecting religious archetypes doesn't mean that they should be or were intended that way. Merely that doing so adds a layer of depth to the film that makes it more satisfying.
Not sure what to do with these references to earlier drafts/titles/storylines. As has come up repeatedly in other threads such concepts as "writers intent" and unused material are pretty much bunk at least within the trek canon. We really would have a very different trek universe if all of those things had been kept in place, not necessarily worse, but factually different. All you are demonstrating there is that at some point there was an intent to include religious themes into the title. An intent that was dropped, very possibly to avoid the very allusions you are making.
I think the viewpoint you are putting out there that the film used religious archetypes to frame the story is definitely worth considering and interesting, one I hadn't fully though about before. I'm just not comfortable with it being an assertion rather than an interpretation. If you had phrased it subjectively rather than objectively the underlying assumptions behind your post would have read very differently (for me at least).
As I said it's very easy to see the film very differently and many of the examples you give as religious references were things I personally had long felt had a very different purpose. I don't claim my own take is somehow "correct", merely that what I took home from it was somewhat different and that certain examples of the medium seem well disposed to that almost "reflective" quality of giving the viewer as much of a personal insight as an intended message.
Thought experiment, just for fun, just how easy is it to find allusions to metaphysical concepts in places they probably were not intended? How easily could we find similar references on a much more clearly blank slate?
You and are totally of the same mindset when it comes to canon I suspect...I also notice that the nature of Internet forums is biting me on the bum here and leading to misunderstanding.
The holy triumvirate...is a jokey way of referring to the characters. It has no bearing here.
The other stuff..well, the simplest answer to any question/discussion about this or things like it is: because the writer wrote it that way.
Then we have the in-universe reason: she stepped in front of Spock.
Then what I am putting forward an interpretation of (these things are always evidence based opinions after all): why the writer chose to do it that way.
In terms of what the things I am talking about bring to the story, well, despite it being more religious symbolism, it actually makes more humanist than it would be without them, by using religious symbols to tell a humanist story....we get a story ride with symbolism bringing the religious and mystical to mind....in which a being finds out that not only is itself fallible, but it's creators too are merely fallible beings....rather than disappointment though, or a breakdown after 'losing its faith' so to speak, it then goes on to be something greater than itself, which in itself becomes it's 'going to heaven' moment...even if it isn't quite what it suspected. Framing all of that in the parent/child theme you already mention, it suggests a non religious approach to life after death...
You attain wisdom and experiences, then pass it on to your children and into the future, and enrich the lives of those around you (Spock in this case directly, and indirectly, Kirk, who gets his ship back...you can also include Ilia and Decker who get a very odd kind of 'marriage' and a very odd classical kind of situation with V'ger being both their progeny and part of themselves, yet also totally outside of that.)
It gives it a very mythic feel, by using that symbolism, and I think, given the draft titles and some of the overt stuff still in the script and film, may have been the writers intent or inspiration.
It's not cast in stone, but I think there's plenty of evidence to make it a valid reading, and little to directly contradict it.
'why did V'ger take Ilia not Spock?
Because Ilia is the virgin mother figure. (at various points she's symbolically Eve, Mary, Mary Magdalena, Isis and probably a whole host of stuff the well travelled Roddenberry knew but I don't.)'
Some of the metaphors are pretty heavily there, other are supposition based on those that are there and my understanding of how to go about crafting a story (well, one of the ways.)
I won't lie, I hadn't thought too deeply about it till this discussion. It's been interesting. I recently read the making of, and no one was really sure why the statue Ilia was being stuck in....now I have a decent working theory as to why.