The way I see it, the qunari plan was rather foolish, why should the inquisition let their people die. If the qunari are going to be stubborn and not allow the inquisition forces to protect the shore they can say bye bye to their little ship.
That's because the Qunari decided to show off by sending in a huge, lumbersome and dreadfully slow dreadnought to sink a dinky little sailing boat, rather than a small, manueverable corvette that could have probably avoided enemy fire entirely?
Otherwise, this was a test and the dreadnought was sent in for that very reason, knowing that it might end up as collateral damage?
If the Inquisitor and Bull save the ship, they've proven that the Inquisition understands the Qunari way of thinking and the Bull has reaffirmed that he's bound to the Qun, whereas if they spare the Chargers, they've failed the test and Bull has proven he's gone native?
Really, I could see them doing something like that, it's a rather efficient way of gauging two birds with a single stone?