Nothing wrong with reading between the lines! I think you have the dynamics down (though I still think they wanted it to be a somewhat tragic end, and botched it), but it's been a while since I saw the movie so I have no way of working out the throughlines. It was definitely mixed somewhere between horror and action but it just didn't bridge the gap terribly well.
Had I been hired to write the movie (that is, my author's intent), I would have had a slightly more boring storyform (and I would have cut ALL of the Jekyll nonsense):
RESOLVE: Change (Nick stops selfish behavior and sacrifices himself)
GROWTH: Stop (Nick stops his recklessness)
APPROACH: Do-er (Nick is impulsive and reckless when it comes to his job -- shooting the rope, etc.)
DRIVER - Action (Discovery of the Tomb; The Mummy is released; The Mummy is Captured; Jenny dies; Nick sacrifices himself)
LIMIT - Optionlock (I like what you said about every remaining curse being destroyed, I'll keep that)
OUTCOME - Failure (Nick is cursed with the evil, ensuring the Mummy will live on)
JUDGMENT - Bad (Nick is forever separated from Jenny)
OS THROUGHLINE: Activity (Finding the Sarcophogus/Studying the Mummy/Chasing the Mummy)
OS CONCERN: Obtaining (Capturing the Mummy/Destroying the Evil)
Since Nick is apparently lacking any real MC throughline, I'll have to create one. To fit in with the IC throughline, I'm going to make a few changes to the narrative.
MC THROUGHLINE: Situation (Nick is a mercenary for hire, stuck paying off debts with one-off jobs that see him traveling the world and taking out 'bad guys'. Until his debt is paid off, he's stuck in that role.)
MC CONCERN: The Future (Nick's future is nothing. He cannot imagine settling anywhere, having become too accustomed to traveling around the world every other week.
I'm going to cut the Jake Johnson thing out, and just make Jenny the solid influence character with a determined belief that man is the monster in the world, forcing Nick to reconsider who he's working for.
IC THROUGHLINE: Fixed Attitude (Jenny believes that mankind should not play God, as it only creates monsters. Her beliefs are in direct conflict with the archaeologists and scientists she has worked for and befriended.)
IC CONCERN: Innermost Desires (I'd need a little think about this one.)
And the RS is obviously going to be a romance, but I won't go into that.
Anyway, just my little take on what the story could have been.