InGen extracting the Indominus? That would have been quite an operation and not one of the most discreet. Which part of the island is turned into a warzone?
As for the mentioned organization in my story, it's not exactly the ACU and is called the Grey Guard, after the dark green-grey colours of their uniforms. Like it, it helps with Jurassic World's security, is sometimes tasked with capturing loose animals, Hamada is the commanding officer on Nublar... but they are not part of Masrani Global, though the latter are among its financial backers. It is actually a paramilitary organization that work first for the United Nations (through the Costa Rica government) and whose first and main role is to guard the Five Deaths and their wildlife (thus, Masrani Global use them at Nublar as PMCs). In terms of aesthetics and mentality, they are quite different from the ACU of the 2015 film.
Interesting premise, as it explores the respective relationships between the ACU, Masrani and InGen. So this story would take place in parallel to the latter parts of the Jurassic World incident? Do you plan to make other illustrations of it or even write it?
In a JW fan-novel that I recently completed, I also had a subplot where the organization that replaces the ACU in my story ends up having a conflict against InGen Security amidst the fall of Jurassic World but for different reasons than those you named (more out of personal vendetta than loyalty to Masrani).
Armies might be word too strong for a dozen of proceratosaurs and 23 raptors. Lol.
But yeah, it's true that the scene has thrilling elements. The whole Haunted Mountain episode is basically Aliens meets Tolkien meets Tomb Raider.