Trying to deduct this with some logic, suspicion and trying to get my head into the story:
Noemi's role
I see Noemi as the counterbalance for Bei. Not the Vishans, but the Shivans speak to Noemi. The blueprint she received is probably a perfected version of ETAK. She can learn to talk with the destroyers, the late elder probably wanted to warn Noemi to not listen to the dark gospel and morbid ballads of they who are the Shivans. If Noemi is a great destroyer, (Sam) Bei is possibly a preserver (taken literally with the Sanctuary 'preserving survivors' from the other universe) who may lead remaining humans to a future.
Also the Shivans spoke of this being their second try I think, so I assume that their first try was perhaps Bosch who similar to Noemi may have been told to destroye the GTVA. It often takes a bastard or ***** to make hard choices, so that those whoever remains can build a better world from the ashes. Alternately they meant the ancients.
A garden overgrown with weed can look beautiful to the eyes of the beholder, but it can never flourish until you cut down the weed. Often the weed is entangled with the plants you adore and it requires cutting both the plants and weed down to have the garden flourish forever without the weed ever coming back.
Anita Lopez
Anita loves her crew and seems to be a bit of a Ng'mei: she's a mother hen and her people follow her blindly into life; into death. Steele probably shook her awake when she took his order to engage the enemy risking most of her crew and Anita may seriously doubt if she's on the right side or not now. I got a gut feeling that Anita may swap sides later on, but I might be wrong. Her crew'd follow her blindly I'm sure.
The Informant
I'm pretty sure the informant is (former) Admiral Thea Carey from the GTD Temeraire. What role she plays from now on I do not know, perhaps someone will help her escape confinement: perhaps Lopez or someone sent by Lopez. I'm not sure if the Temeraire would follow her example. Alternately she may die as example, though that'd be an anti-climax. A third option is re-education or brainwashing, something which'd be sad and I think would not do the Carey character justice (but it is an ironic faith).
Lorna Simms
I slightly suspect Simms to have died in Noemi's arms. Noemi admitted loving Lorna, which can mean anything: in a harsh period love isn't always about butterflies and crawling under the blankets, it can be comfort with having someone to support on. Lorna realized she was not alone right there and then and I think she gave up living the moment she said she'd train new pilots on the Indus again: it sounds like she'd live an empty life waiting for death. If Lorna indeed did die then for once she wasn't the one to have someone die in her arms but instead died in someone else their arms, in Noemi's knowing she was with the person she could and did love. Dying (especially that way) was very merciful for the woman with a deathwish. We'll see if she made it through.
The faith of the Indus and the Feyadeen
The faith of the Indus is questionable and depends on the Feyadeen. If they want to utilize Noemi's anger, they'd probably blow it up or let it drop into the sun after retrieving Noemi. "Come to the darkside" so to say, feed the little destroyer her anger. Alternately they may just want to sanitize the ship. It's probably beyond repair even if recovered, most crew may be beyond help and the Feyadeen can stay secret for a reason. If the Feyadeen intend to keep Noemi from falling, they may try to salvage the ship and to safe Simms' life, or alternately lie about Simms being alright even if the latter might not be true.
The Feyadeen's intentions and the faith of the Indus is least clear to me, which is a good sign, it means the Feyadeen and their intentions are as mysterious as they are supposed to be! They can be saints, or for all we know a second Hammer of Light. Exciting!
The secret project
I'm guessing that the secret project which needs so many logistical support may be a final exodus to find humankind's destiny. After all if humankind is the great builder, restorer or whatever, their faith lies with the entire galaxy or universe! Not just within the Sol system or even GTVA held territory. They're packing their backs perhaps. It's the only thing I can come up with. The vasudans may be the great chroniclers, remaining the philosophers to write about this ascension, much like they once tried with the ancients (who seemingly didn't quite make the cut).
Faith of the GTC Duke and other vessels
Here I assume three options:
1) Reverse engineering: The Federation may finally build their own version of beam weaponry.
2) Infiltration: Slap a new ID and security codes on her, and you can just perhaps quietly sail into GTVA space to either do damage or to retrieve someone (maybe Thea Carey?) or something. I can somehow see Al'fadil being talked into reason by Bei. Or maybe not.
3) Escorting and/or masquerading: They may simply form an escort for the logistical vessels. Maybe they did something funky to their beams or wish to masquerade as the escorts of a logistical vessel they might try to replace. Imagine being able to sabotage or even hijack a unaware destroyer which docks with the logistical vessel. It wouldn't hurt to have a Titan or even Hecate in the fleet. Hijacking seems unlikely though, it doesn't fully fit in the flow of the federation's actions.
My speculations thus far.