I agree that M can’t really be the IC simply because not enough of the ‘heart’ of the story is in their relationship (and, really, no audience member would think that theirs was the RS.)
However the challenge for me conceptually is that deriving a change of resolve for Bond from one of being driven by passion to being driven by logic and by extension that Vesper is steadfast with an approach involving logic simply isn’t borne out by the story itself. She begins the film arguing the need to be dispassionate (including all the reasons she won’t fall for him) and ends by falling in love with him and changing her approach (she knowingly sacrifices herself in order to save his life–that’s the deal she made with the secondary bad guys.)
Again, you could find an argument that by virtue of her apparent betrayal it makes James go back to being an emotionally distant individual (and, through that return, make a change of approach to one of pure dispassion) but it requires tremendously circuitous logic that could be used to make pretty much any argument about the relationship and its effects.
If I just look at the story from the standpoint of their actions and arguments, Bond starts the story showing his comfort with killing for Queen and Country (the opening shows him earning his second kill.) Vesper challenges him throughout the movie by undermining the persona he puts out to the world and, equally, by her revulsion over his willingness to kill. At the initial end of the movie, he not only falls in love with her but, because of that love, decides to quit the service. She’s convinced him to let go of violence and duty (“I’ve got no armour left, whatever is left of me is yours.”) When he believes she’s betrayed him and the government, he goes back to being who he was before–in fact, he doubles-down on being even more emotionally distant than at the start.
You can argue that the real evidence of resolve is that he doesn’t kill the last guy in the final shot of the film, but I think that’s really stretching things. If Vesper is the IC, then the things that happen in that relationship point to the conflict being over whether Bond will forever be a cold-hearted killer who only wears his slick playboy demeanour like a suit of armour. Since he starts that way and ends that way, he would seem to me to be steadfast.
If I were to temporarily suspend the Dramatica’s underlying structure (dangerous, I know!) then I would say that this is simply two stories jammed together. In the first, Bond begins as a cold-hearted emotionally distant killer. His relationship with Vesper changes him to someone who is willing to set aside duty in order to be happy and to be a complete person. The second story (which is very short) begins shortly after–Bond and Vesper are starting a new life when he discovers she hasn’t been honest with him. That dishonesty, regardless of reasons and outcomes, causes him to give up on love entirely.
Sorry for the long post (and for what I imagine are any numbers of misinterpretations!)