Alyssa was correct on one thing - no one is going to follow Hultressa in trying to command the Ark. She's running around with ex-slaves, Asur especially, and none of the Coven is going to be swayed to her side. Kerillian has expressed blatant and open disdain for the Cult of Khaine, and it is only through weight of total loss of Cult leadership/seniors/veterans/regulars as well as the trauma of losing the Temple of Khaine to Slaanesh plus the threat of being killed and being newly inducted that the Witch Elves currently following her around were convinced to do so. The greater majority of all Druchii on the Ark would not be so easily pressed by Kerillian, and would try to kill her for the sword anyhow. Hultressa does not want to remain on the Ark, she'd rather see the entire thing destroyed. Not to mention that Hultressa alone could not possibly command the Ark's movement or function without support from the rest of the Coven, especially now that the Ark's Anchorstone Complexes are in damaged condition through the total catastrophic loss of one and damaging of all the others in compensation with further damage to one of them.
The goal for Hultressa is and has always been to leave the Ark, not to command it, not to take control of it.
You do not have the forces to compel the entirety of the Ark into submission, because they have reached a frenzied pitch that will not allow it without the hyper-fast shock of loss and capitulation enforced during Salkalten thanks to the Eonir and Nordland coalition working with Ostland in absolutely overwhelming them all from a pincer maneuver after their forces got blasted at the walls.
At the beginning of this, both Natasha and Frederick both agreed that they knew they would have to leave any number of innocents left on the Ark in almost every scenario of attempting to get off the Ark, even if they got some slaves and others out with them.
There are no attempts to justify IRL war crime behavior or genocide here at this time please and thank you. For one thing, this is Warhammer, where children and innocents are burned at the stake or killed with blades because of mutations or suspicions of magic or heresy, that is part of the grim dark nature of the setting based around IRL inspirations and IC extrapolations and situations. It's a sad and bad thing, but it happens. Rampaging ex-slaves have not, historically, been terribly forgiving and kind to their former captors, especially if they are quite literally inhumanly cruel and monstrous to them with magics and potions and poisons that go beyond anything manageable IRL. Even the Asur have not been able to 'perfectly' save every single slave on a Black Ark when they take one down, neither have the dwarfs when they were able to bring enough dreadnoughts to bear and blow one to pieces with cannon fire. Nor did Gotrek and Felix, canonical Warhammer heroes, when the Harp of Ruin exploded and took an Ark down with it. They certainly felt awful and bad about all the innocents left on the Ark, but sometimes, you just can't save everyone. That doesn't make it a justification for war crimes or genocide, also this is one Ark, there's still plenty of Druchii elsewhere and more Arks besides.
Natasha is born of the Gospodars, who were once Kurgan, but then came and conquered Kislev at the head of Miska the Slaughterer, the Last Khan-Queen of the Gospodars.
Frederick is born of the Ostlanders, who were once the Udoses, who have one of their main historical features in the past being ecstatic about a burning coastline of Norsii peoples - men, women, elders, children - long into the night.
I'm not saying these are 'good' things, and rather on the whole I would think I've shown how Frederick and Natasha are perfectly capable of empathizing and being soft-handed towards at least one of the children of the Druchii, but they are not Gods capable of snapping their fingers and solving the 'issue' of the Black Arks in total perfection. Additionally, they are perfectly capable of being ruthless. It's even in their Trait list. And the sheer military threat of a Black Ark is such that there are plenty of people who would likely at the end of the day accept just blowing up an Ark as the cost of preserving many more lives elsewhere. Druchii kill Druchii all the time, they have whole hosts of assassins dedicated to it, up to and including children of their political enemies, contracts with Khainite assassins and all that go deep wide and long. There are Druchii killing Druchii right now on the Claw of Dominion, and likely every single Black Ark in existence. When House Cruelbarb went down, there wasn't a lot of 'sparing' going on there on the part of the Alyssan forces, nor for the House who's Tor the warband took over, who got slaughtered wholesale by another House rising up to replace them, who was in turn taken down by the warband. I even made strong allusions and references to some of the slaves being very certain about killing all the Druchii in the Tor, even smaller ones, but in the chaos no one was sure precisely who did it because of how angry the rush up the Tor was. And that's a cold, dark, terrible thing to have happened, but it did, because ex-slaves of the Druchii are ex-slaves of the Druchii and not all of them possessed of the sheer strength of character and nobility as, say, Roland.
So.
1. None of the Asur want to remain on the Ark at all, and would prefer to get off of this millennia tainted-rock. Also, Sadrina the Handmaiden of the Everqueen is a highly symbolic figure of all things Druchii hate to the point that killing her off publicly and violently and torturously would be one of the top requirements in the case of actually making a serious attempt at commanding the Ark's populace and even then would be extremely difficult for various reasons even if it came to pass, which is not likely because Hultressa wants Sadrina's endorsement to the Everqueen to help save Gwendolyn's soul.
2. Hultressa wants off the Ark as quickly and violently as possible after retrieving Frederick and Eldyra.
3. Kerillian hates the Ark, hates the Cult of Khaine as it is in Druchii interpretation, and frankly hates the culture of the Druchii as well, especially after she got locked up and tortured herself. She also does not have the religious or political juice to sway the Druchii as a whole, and would not bother making the attempt anyway, even with the sword, because if she dies then another proper Druchii could pick it up as well.
4. Everyone else in the warband wants off the Ark as well.
5. The Ark is extremely damaged, the Coven depleted and highly likely to refuse to aid Hultressa in command and control, and she's not going to explode her brain and soul trying to run it when she has her daughter to worry about.
6. The Cult of Mathlann is the one with the boats, and they aren't going to hand them over to Hultressa or Kerillian in anything approaching peacefulness.