Cobbling together some of my earlier posts to reply:
A surprising number of fans feel that this is some manner of test for Bull set up by the Qunari. I find this highly unlikely - he was a good agent, but I doubt they are willing to risk a dreadnought and its crew just to test the loyalty of that agent. It's a terrible price for the Qun to pay if Bull doesn't choose the Qun over his current life, and the Qunari (as far as we can tell) do not waste anything if they can avoid it.
A number of other fans feel that you, as a the player, should not look at this as anything more than you (again, as the player and not the Inquisitor) choosing the direction of Iron Bull's narrative. I find it difficult to do that myself; I have to frame this choice in terms of how the Inquisitor would do it in the moment in order to make the whole scenario feel right. As a player, I inevitably feel I made the wrong choice regardless of which one I choose. I feel I let the Inquisition down if I sacrifice the dreadnought, and I feel I let Bull and the Chargers down if I do not.
If you're looking at this from a narrative perspective in so far as developing a canon storyline for your Inquisitor:
Sacrifice the Dreadnought:
- No alliance with the Qunari - this may or may not have consequences for southern Thedas later. No Ben-Hassrath intelligence being shared, no Ben-Hassrath War Table missions. Qunari may be unlikely to make similar offer in the future.
- Bull's Chargers available - Krem & Co will be available for other War Table missions. From a narrative perspective, this can also have unspoken effects on the morale of the Inquisition soldiers. Both because the Inquisitor was unwilling to sacrifice her/his people, and because the Chargers are very well respected amongst the other troops. Also, keep in mind the Chargers are much more than the five or so you meet at Skyhold. It's a much bigger company than that, you only meet 5 of them.
- Iron Bull declared Tal-Vashoth by the Qunari. He questions his himself and his ability to keep his composure. Fellow companions all try to sooth this by saying they will help him, that they will be there for him if needs them. He seems to appreciate this. His overall mood does not change that much; his introspection comes out largely when other companions ask him questions.
Sacrifice the Chargers:
- Alliance with the Qunari - this may or may not have consequences for southern Thedas later. Ben-Hassrath intelligence willingly shared, Ben-Hassrath War Table missions. Long strings of operations involving tracking down and destroying Venatori operatives and their missions within Thedas take place because of this cooperation. While you do not see them in action, mission reports indicate that the Ben-Hassrath are committing their people to this, not just forwarding the intelligence to the Inquisition.
- Bull's Charges unavailable. Krem & Co gone, no War Table missions for them. From a narrative perspective, this can have unspoken effects on the morale of the Inquisition. The Inquisitor choose an Alliance over part of her/his people; this may have the effect of the Inquisitor appearing imperious and/or willing to sacrifice in the short term to win the long game. The individual military will probably not be as pleased, but the nobility and backers of the Inquisition may have more respect.
- Iron Bull remains with the Qun and is happy that the Alliance is working. However, the loss of the Chargers wrecks him. He withdraws and is inconsolable over their sacrifice. His demeanor becomes much more Qunari outwardly; Solas and Bull snap at each other constantly. At the end, he seems okay about returning to the Qun - this may or may not be genuine as he's had a lot of time to contemplate since the events on the Storm Coast.
Sacrificing the Chargers, in my opinion is the better choice for the Inquisition overall, and it's the hard choice that leader of the Inquisition needs to make.
You, as the Inquisitor, have a responsibility to the Qunari. Assuming that no hidden "we are testing Hissrad's loyalty" subterfuge exists and this is exactly what it seems to be, the Qunari brought the dreadnought in to sink the Venatori vessel under the condition that the Inquisition provide ground support. That was part of the arrangement in having this operation take place. They would not have risked the vessel and its crew had the Inquisition not agreed to support it.
Abandoning this responsibility is essentially saying, "once the Venatori ship is sunk, you are on your own. Expect no further support from the Inquisition."
If you do not protect the dreadnought, you're going to lose the alliance because the Arishok, or Ariqun, or whomever, is going to ask Gatt what happened at that battle. And he is going to tell the Qunari leadership that the Inquisition chose to retreat rather than honor their arrangement.
If this was not Bull's Chargers on that other hill, and just some nameless Inquisition soldiers under Cullen's command that the Inquisitor had never spoken to before, would you balk at sacrificing them to ensure the operation is successful? The fact that you have met them should not alter your Inquisitor's position. If it does, then your Inquisitor has no business making military or diplomatic decisions and should leave them to Cullen and Josephine, respectively.
Because if that's how your Inquisitor honestly feels, that the Qunari vessel you agreed to protect is not worth protecting at the cost of some of your people's lives, then you are not prepared to honor your half of the arrangement and you're better off telling Bull not to bother arranging the operation when he first suggests it. You become the deceitful party otherwise. Lives were going to be at risk from the moment you accepted Bull's offer to work with the Ben-Hassrath on this. If you were not prepared to lose some of them for the alliance, you should have never agreed to work with the Qunari in the first place.
To quote from elsewhere, "To be a good soldier you must love the army. But to be a good officer you must be willing to order the death of the thing you love. This is a very hard thing to do" - Michael Shaara, The Killer Angels