I agree with you about the cue just below the London bombing with the London Calling theme and John Harrison's theme. It is my favourite unreleased cue.
I was never content with referring to that theme as "Dark Side of Starfleet" but it was the best I could come up with. I think its statements during scenes where Marcus didn't appear threw me off but your assessment that those scenes are indirectly linked to Marcus makes sense. I agree that calling it Admiral Marcus's theme is neater (the theme no longer appears after he is killed), although within the context of the movie Admiral Marcus and "Dark Side of Starfleet" are the same.
The scene where Harrison attacks the Starfleet meeting is the only major action cue that is unreleased but it is so heavily drowned out by sound effects that I can't comment on the music. I didn't hear any thematic material however. I really expected to hear a cool statement of John Harrison's theme during the shot of him looking at Kirk as he is transporting off his jumpship but Giachinno decided not to do so.
It's also amusing that most commentry about this OST I've read is assuming that a deluxe edition is a certainty. However from a profit-making point of view, I would be very surprised if Verese doesn't release a deluxe edition within a year to repeat the double-dip of the ST09 score.