Shot weight vs shot size
Actually, although the doomwhale is a very powerful weapon, it's not that much more powerful than the krakens, and the lightness of a merchant ship's structure will actually work against its destructiveness.
I can't remember if the kraken -- or the carronades carried by the Kraken, in this case -- are the "old" krakens or the newer, somewhat lighter model that Howsmyn is producing as of By Schism Rent Asunder, but assuming that they are the old 38-pounders, then the shot diameter is roughly 6.8 inches, whereas the doomwhale's shot diameter is approximately 7.5 inches. Despite the fact that it is roughly 32% heavier than the kraken's shot, its diameter has increased by less than 11%, and is really more diameter than weight of shot that is going to be the decisive factor in this case. Mind you, having a heavier round shot certainly isn't going to hurt anything, but unless it hits a major structural member, or a mast, it's probably going to simply punch right through the hull planking, and may well actually punch completely through the ship and land in the water on the other side. Anyone who gets in its way will undoubtedly be killed, and the heavier shot will produce more (and larger) splinters from a given thickness of hull. In this case, Kraken is probably (note the clever equivocation) more heavily built than the galley, because Kraken is intended to stand the pounding of blue-water commerce, whereas the galley is essentially a coastal design which is maximized for speed and mobility under oars rather than for toughness. Despite that, she doesn't have the incredibly thick scantlings (side timbers) which are built up to serve as "armor" and hull stiffeners for true warships. So it's unlikely that splinters are going to be the threat to personnel aboard her that they would be aboard a regular warship of the Charisian Navy.
The result is that the only real difference between what a shot from one of the carronades would do and what a shot from the galley's doomwhale would do is going to be the difference in diameter of the holes they leave in the hull on their way through, and a single hit from a doomwhale isn't going to come even close to sinking a wooden ship. (Wooden ships were incredibly difficult to sink using nonexplosive round shot simply because of how small the holes were; the fact that most of them were at or above the waterline, where they either constituted no flooding the threat or at least could be gotten at quickly for repairs; and how readily flooding could be controlled by pumps while the holes were plugged.) The galley's captain is thinking in terms of engaging an unarmed merchant ship, and he intends to use his heaviest, longest-ranged artillery in order to make the point that he has the range to engage not simply the first target on his list but any of the others if they turn around and run. He's also never seen the new, improved artillery in action, and so he doesn't have any real grasp of the difference in rates of fire or expect his opponents to be thinking about the difference in rates of fire. Unless he's able to hit something absolutely critical with his first shot or two, it's going to come down to numbers of guns and rate of fire far more than to the absolute weight of shot of the guns involved.
Of course, I'm not saying how the action will work out an "real life," now am I?