Well, they clearly weren't "perfectly good battlecruisers" if ComStar had to cannibalize one to keep the other going. ;)
If I recall Masters & Minions correctly, Gregory Zwick, who was of course Beresick's deputy, made his name recovering a Naga from the Deep Periphery. So perhaps what Morgan wasn't meant to know was the scope of ComStar's targeted WarShip recovery operations. Beresick makes it sound as though they just stumbled on the two ships.