Maybe, but you forget one thing. The secondary blast that followed the initial shockwave didn't give them any time to repair themselves. You saw it yourself: when the second blast went off, the PLANETS were destroyed, and it came a matter of moments after the initial wave.
the planet-killer wave, that was the first wave. (This is my whole point, they lived through a blast that was capable of cracking planets.) The second is something we've got no clue as to what it is or what it did.
I don't think I'd call those hulls intact. They looked fused, melted, and utterly unrecoverable. In fact, they looked destroyed past the point of being blown apart. At least when you blow up some chunks might come out fairly intact. These guys were uniformly cooked.
They were still perfectly recognizeable as what they had been. That makes them pretty much intact by any standards. The shots we saw suggested the color patterns
on the hulls were still the same. The weren't melted or charred. The turrets were probably a lost cause, but the hulls were intact. They were damaged, certainly, shock and spalling and their structural members probably have a dozen fractures each, but they're not fused and melted. That doesn't hold up.
You don't necessarily have to blow a ship to pieces; you have to render it unsuitable for life. Usually you can do that in one of two ways, A: like you said, blow it to pieces, or B: Destroy the life-support. After all, a ship is only as good as the one (or ones) flying it, so if they're dead, the ship is dead, and the crippling nature of the shockwave probably killed them just by the loss of life-support.
Killing the life-support systems aboard a ship will not render it unliveable in a combat-effective amount of time. A modern submarine that loses its air recyclers can keep going for hours. FS ships, with their huge internal volume and comparatively small crew, might last for weeks. You have to put holes in the hull to kill crew quickly. Available evidence suggests that (being very very
generous of it, you could also say available evidence suggest no crew losses at all aboard the Deimos) any crew from the side hit with the shockwave to amidships aboard those ships was dead. That still leaves slightly less than half (counting compartments which have open space on the midships dividing line).